MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Computational Biology and Chemistry' source. Fri, 19 Mar 2010 17:37:27 +0100 http://www.medworm.com/index.php?rid=3347311&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20206582%26dopt%3DAbstract We describe an algorithm to avoid steric violation (bumps) between bodies arranged in a hierarchy. The algorithm recursively directs the focus of a bump-detector towards the interactions of children whose parents are in collision. This has the effect of concentrating available computer resources towards maintaining good steric interactions in the region where bodies are colliding. The algorithm was implemented and tested under two programming environments: a graphical environment, OpenGL under Java3D, and a non-graphical environment in "C". The former used a built-in collision detection system whereas the latter used a simple algorithm devised previously for the interaction of "soft" bodies. This simpler system was found to run much faster (by 50-fold) even after allowing for time spent on... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3347311 Thu, 04 Feb 2010 00:00:00 +0100 3347311 http://www.medworm.com/index.php?rid=3135897&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20042369%26dopt%3DAbstract Authors: Tang D, Zhu Q, Yang F Serial analysis of gene expression (SAGE) is a powerful tool to obtain gene expression profiles. Clustering analysis is a valuable technique for analyzing SAGE data. In this paper, we propose an adaptive clustering method for SAGE data analysis, namely, PoissonAPS. The method incorporates a novel clustering algorithm, Affinity Propagation (AP). While AP algorithm has demonstrated good performance on many different data sets, it also faces several limitations. PoissonAPS overcomes the limitations of AP using the clustering validation measure as a cost function of merging and splitting, and as a result, it can automatically cluster SAGE data without user-specified parameters. We evaluated PoissonAPS and compared its performance with other methods on several... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3135897 Mon, 28 Dec 2009 00:00:00 +0100 3135897 http://www.medworm.com/index.php?rid=3033886&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19939735%26dopt%3DAbstract Authors: Aita T, Nishigaki K, Husimi Y In vitro molecular evolution creates a lot of peptide aptamers that bind to each target protein. In many cases, their binding sites on a protein surface are not known. Then, predicting the binding sites through computation within a reasonable time is desirable. With this aim, we have developed a novel system of fast and robust blind docking of a peptide to a fixed protein structure at low computational costs. Our algorithm is based on the following scheme. Representing each of the amino acid residues by a single point corresponding to its side-chain center, the structure of a target protein and that of a ligand peptide are coarse-grained. The peptide, which is described as a flexible bead model, is movable along the grid-points which are set surro... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3033886 Wed, 04 Nov 2009 00:00:00 +0100 3033886 http://www.medworm.com/index.php?rid=3033885&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19939736%26dopt%3DAbstract Authors: Zawaira A, Gallotta M, Beeton-Kempen N, Coulson L, Marais P, Kuttel M, Blackburn J In this work, a model for the interaction between CYP2B4 and the FMN domain of rat P450-oxidoreductase is built using as template the structure of a bacterial redox complex. Amino acid residues identified in the literature as cytochrome P450 (CYP)-redox partner interfacial residues map to the interface in our model. Our model supports the view that the bacterial template represents a specific electron transfer complex and moreover provides a structural framework for explaining previous experimental data. We have used our model in an exhaustive search for complementary pairs of mammalian CYP and P450-oxidoreductase (POR) charge clusters. We quantitatively show that among the previously defined ba... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3033885 Sat, 31 Oct 2009 00:00:00 +0100 3033885 http://www.medworm.com/index.php?rid=3000866&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19910254%26dopt%3DAbstract We present results on such effects in finite-sized biological data sets and point to future research directions. We are most of all concerned with bacterial, ribosomal proteins as a prototypical example in molecular evolution. We compare to previous published suggestions, give an empirical formula, and propose a protocol to guide future research projects. PMID: 19910254 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3000866 Fri, 23 Oct 2009 00:00:00 +0100 3000866 http://www.medworm.com/index.php?rid=2992898&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19906563%26dopt%3DAbstract Authors: Furman DP, Oshchepkova EA, Oshchepkov DY, Shamanina MY, Mordvinov VA The computer system SITECON was used to study the regulatory regions in the transcription factor genes expressed in the activated macrophage and the genes of the proteins mediating the macrophage involvement in the immune response. Dioxin responsive elements (DREs), the specific sites responsible for expression regulation of the genes involved in the cell response to dioxin, were found in these gene regions. Thus, the role of dioxin in activity regulation of the genes involved in development of the immune response can be regulated both directly, by the transcription complex containing dioxin as a ligand, and indirectly, via intrinsic transcription factors.The double regulation, via DRE and the binding sites f... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2992898 Fri, 23 Oct 2009 00:00:00 +0100 2992898 http://www.medworm.com/index.php?rid=2978086&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896904%26dopt%3DAbstract We examined 75 complete microbial genomes using the Tm Index, and the analysis clearly differentiated hyperthermophilic from mesophilic microorganisms on this global genomic basis. These results are consistent with the previous hypothesis that hyperthermophiles express a greater number of high Tm proteins compared with mesophiles. The Tm Index will be valuable for modifying existing proteins (enzymes, protein drugs and vaccines) or designing novel proteins having a desired melting temperature. PMID: 19896904 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2978086 Tue, 20 Oct 2009 00:00:00 +0100 2978086 http://www.medworm.com/index.php?rid=2968183&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19889579%26dopt%3DAbstract Authors: Füllbeck M, Gebhardt N, Hossbach J, Daniel PT, Preissner R Apoptosis, the programmed cell death, is a highly regulated process, necessary for normal development and homeostasis of the functions of organisms. The Bcl-2 inhibitors BH3I-1 and BH3I-2 were used as lead compounds to find possible Bcl-2 or Bcl-X(L) inhibitors by using computer-assisted screening with our in-house database, containing more than four million commercially available molecules. Identified compounds were further investigated regarding their possible application as a drug. PMID: 19889579 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2968183 Mon, 12 Oct 2009 00:00:00 +0100 2968183 http://www.medworm.com/index.php?rid=2968181&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19889581%26dopt%3DAbstract Authors: Nair TM Alternative splicing of human pre-mRNA is a very common phenomenon and is a major contributor to proteome diversity. mRNA isoforms that arise as a result of alternative splicing also provide a more complete picture of the transcriptome as they reflect the additional processing a pre-mRNA undergoes before being translated into a functional product. It has been reported that molecular alterations of cells can occur as a result of the differential expression of mRNA isoforms, resulting in cancerous or normal tissue. Quantification of mRNA isoforms can thus be used as a better indicator in distinguishing a normal tissue from a cancerous tissue. In our earlier study we had used mRNA isoforms expression to identify biomarkers for prostate cancer (Li et. al, 2006. Cancer Res.... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2968181 Fri, 09 Oct 2009 00:00:00 +0100 2968181 http://www.medworm.com/index.php?rid=2968182&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19889580%26dopt%3DAbstract In this study, we examined the effect of hsa-miR-601 on gene expression changes in human lung cancer cells A549. To achieve this, DNA microarray and global pathway analyses were performed on hsa-miR-601 introduced cells for two successive days. Gene ontology analysis revealed that the effect of hsa-miR-601 over-represented the negative regulation of translation/translational initiation, whereas GenMAPP analysis revealed that several characteristic pathways were changed in hsa-miR-601 introduced A549 cells compared to control short RNA introduced cells. Among them, up-regulation of actin cytoskeleton and down-regulation of Fas-induced apoptosis pathway occurred on two successive days after hsa-miR-601 introduction. Using a luciferase reporter assay, we also showed that hsa-miR-601 specifica... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2968182 Fri, 02 Oct 2009 00:00:00 +0100 2968182 http://www.medworm.com/index.php?rid=2924114&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850527%26dopt%3DAbstract Authors: Crabbe MJ Climate change will have serious effects on the planet and on its ecosystems. Currently, mitigation efforts are proving ineffectual in reducing anthropogenic CO(2) emissions. Coral reefs are the most sensitive ecosystems on the planet to climate change, and here we review modelling a number of geoengineering options, and their potential influence on coral reefs. There are two categories of geoengineering, shortwave solar radiation management and longwave carbon dioxide removal. The first set of techniques only reduce some, but not all, effects of climate change, while possibly creating other problems. They also do not affect CO(2) levels and therefore fail to address the wider effects of rising CO(2), including ocean acidification, important for coral reefs. Solar ra... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2924114 Fri, 02 Oct 2009 00:00:00 +0100 2924114 http://www.medworm.com/index.php?rid=2877336&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19815464%26dopt%3DAbstract Authors: Jin L, Fang W This note points out that the comment article by Kedarisetti et al. (2006a, refer to 'K-comment' hereafter) was based on the code analysis with methodological and mathematical errors. The incorrect modification of the original code and FDOD method has resulted in the wrong conclusions in K-comment. PMID: 19815464 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2877336 Tue, 15 Sep 2009 23:00:00 +0100 2877336 http://www.medworm.com/index.php?rid=2839375&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782003%26dopt%3DAbstract Authors: Fiume G, Rossi A, Di Salle E, Spatuzza C, Mallardo M, Scala G, Quinto I MicroRNAs (miRNAs) are small single-stranded RNA molecules that play an essential role in the regulation of gene expression and cell physiology. Gene rearrangements occurring in the miRNA sequence are associated with cancer. The IBTK genetic locus is located in the genomic sequence 6q14.1 that undergoes chromosomal aberration in lymphoproliferative disorders. The IBTK gene encodes the proteins IBtk-alpha, beta and gamma that regulate the B cell receptor signalling through Bruton's tyrosine kinase, which promotes B cell survival and differentiation. Pro-MirII-based analysis predicted four precursors of microRNAs (pre-miR) encoded by introns 17, 21, 26 and the 3' un-translated region of the IBTK gene. Pre-mi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2839375 Sat, 05 Sep 2009 23:00:00 +0100 2839375 http://www.medworm.com/index.php?rid=2797603&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19748831%26dopt%3DAbstract Authors: Song JJ, Ren Y, Yan F High-throughput data have been widely used in biological and medical studies to discover gene and protein functions. Due to the high dimensionality, principal component analysis (PCA) is often involved for data dimension reduction. However, when a few principal components (PCs) are selected for dimension reduction or considered for dimension determination, they are typically ranked by their variances, eigenvalues. However, this approach is not always effective in subsequent multivariate analysis, particularly classification. To maximize information from data with a subset of the components, we apply a different ranking criterion, canonical variate criterion, which considers within- and between-group variance rather than total variance in the classical cri... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2797603 Mon, 17 Aug 2009 23:00:00 +0100 2797603 http://www.medworm.com/index.php?rid=2742161&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19709932%26dopt%3DAbstract We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current method, unlike some of the graphical approaches proposed in the literature, uses the values of the experimental measurements only relative to the geometry of the biochemical reactions under the assumption that the underlying reaction network is the same for all the experiments. The proposed approach utilizes algebraic statistical methods in order to parametrize the set of possible reactions so as to identify the most likely network structure, and is easily scalable to very complicated biochemical systems involving a large number of species and reactions. Th... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2742161 Wed, 05 Aug 2009 23:00:00 +0100 2742161 http://www.medworm.com/index.php?rid=2735194&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19700369%26dopt%3DAbstract Authors: Crabbe MJ, Konopka AK PMID: 19700369 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2735194 Sun, 02 Aug 2009 23:00:00 +0100 2735194 http://www.medworm.com/index.php?rid=2682529&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19656727%26dopt%3DAbstract Authors: Li L, Zhou R, Huang D As a fundamental step of biomedical text mining, Biomedical Named Entity Recognition (Bio-NER) remains a challenging task. This paper explores a so-called two-phase approach to identify biomedical entities, in which the recognition task is divided into two subtasks: Named Entity Detection (NED) and Named Entity Classification (NEC). And the two subtasks are finished in two phases. At the first phase, we try to identify each named entity with a Conditional Random Fields (CRFs) model without identifying its type; at the second phase, another CRFs model is used to determine the correct entity type for each identified entity. This treatment can reduce the training time significantly and furthermore, more relevant features can be selected for each subtask. In ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2682529 Sun, 02 Aug 2009 23:00:00 +0100 2682529 http://www.medworm.com/index.php?rid=2682528&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19656728%26dopt%3DAbstract Authors: Zuk T, Rakowski F, Radomski JP The spread efficiency of influenza virus is significantly affected by several environmental parameters. However, neither the underlying reasons, nor the exact character and magnitude of the phenomena involved are sufficiently well understood. Here we present a probabilistic approach to the virus transmission events. For a sample ensemble, we construct a model of the infectivity as a function of the ambient conditions, and we determine its parameter values on the basis of the available experimental data. PMID: 19656728 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2682528 Sun, 02 Aug 2009 23:00:00 +0100 2682528 http://www.medworm.com/index.php?rid=2682526&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19660987%26dopt%3DAbstract Authors: Lauria A, Ippolito M, Almerico AM Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a public database of measured binding affinities. Further,... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2682526 Wed, 22 Jul 2009 23:00:00 +0100 2682526 http://www.medworm.com/index.php?rid=2682527&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19660986%26dopt%3DAbstract Authors: Lai X, Nikolov S, Wolkenhauer O, Vera J We develop a multi-level model, using ordinary differential equations, based on quantitative experimental data, accounting for murine erythropoiesis. At the sub-cellular level, the model includes a description of the regulation of red blood cell differentiation through Epo-stimulated JAK2-STAT5 signalling activation, while at the cell population level the model describes the dynamics of (STAT5-mediated) red blood cell differentiation from their progenitors. Furthermore, the model includes equations depicting the hypoxia-mediated regulation of hormone erythropoietin blood levels. Take all together, the model constitutes a multi-level, feedback loop-regulated biological system, involving processes in different organs and at different organ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2682527 Wed, 08 Jul 2009 23:00:00 +0100 2682527 http://www.medworm.com/index.php?rid=2668564&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19646926%26dopt%3DAbstract In this study, we present a building block of proteins called order profiles to use the evolutionary information of the protein sequence frequency profiles and apply this building block to produce a class of propensities called order profile interface propensities. For comparisons, we revisit the usage of residue interface propensities and binary profile interface propensities for protein binding site prediction. Each kind of propensities combined with sequence profiles and accessible surface areas are inputted into SVM. When tested on four types of complexes (hetero-permanent complexes, hetero-transient complexes, homo-permanent complexes and homo-transient complexes), experimental results show that the order profile interface propensities are better than residue interface propensities an... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2668564 Wed, 08 Jul 2009 23:00:00 +0100 2668564 http://www.medworm.com/index.php?rid=2668563&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19646927%26dopt%3DAbstract Authors: Nov Klaiman T, Hosid S, Bolshoy A The advancement in Escherichia coli genome research has made the information regarding transcription start sites of many genes available. A study relying on the availability of transcription start locations was performed. The first question addressed was what an average DNA curvature profile upstream of genes would look like when these genes are aligned by transcription start sites in comparison to alignment by translation start sites. Since it was hypothesized that curvature plays a role in transcription regulation, the expectation was that curvature measurements relative to transcription starts, rather than translation, should strengthen the signal. Our study justified this expectation. The second question aimed to clarify the relation betwe... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2668563 Mon, 06 Jul 2009 23:00:00 +0100 2668563 http://www.medworm.com/index.php?rid=2668562&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19647489%26dopt%3DAbstract We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the population. In terms of the total number of energy function evaluations both methods perform equally well, however, PLS has the potential of being parallelised with an expected s... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2668562 Thu, 02 Jul 2009 23:00:00 +0100 2668562 http://www.medworm.com/index.php?rid=2627498&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19617003%26dopt%3DAbstract Authors: Khrustalev VV, Barkovsky EV Total GC-content (G+C), GC-content in codon positions and 0-fold, 2-fold and 4-fold degenerated sites in all coding districts from 10 completely sequenced genomes of simplex and varicello viruses have been calculated by the original "Coding Genome Scanner" algorithm. The low coefficient of correlation (R<0.5) between 3GC and G+C in all coding districts from unique regions (UL and US) of alphaherpesvirus genome is a new criterion of the strong mutational pressure that is the process of increasing the rates of nonsynonymous mutations because of the extreme saturation (GC-pressure) or desaturation (AT-pressure) of third (liberal) codon positions with G and C. Unique regions of HSV1, HSV2, CeHV1, CeHV2, CeHV16 and BoHV5 are under the influence of str... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2627498 Fri, 26 Jun 2009 23:00:00 +0100 2627498 http://www.medworm.com/index.php?rid=2627500&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19616477%26dopt%3DAbstract Authors: He Y, Zhou R, Huang Y, Xiao Y Detection of foldable subunits in proteins is an important approach to understand their evolutions and find building motifs for de novo protein design. Using united-residue model, we simulated the folding of a six-helix protein with a length of 120 amino acids (C-terminal domain of Ku86). The folding behaviors, structural topology and sequence repetition of this protein all suggest that it may have a two-fold quasi-repetition or symmetry in its sequence and structure. Therefore, we simulated the folding of its two halves (1-60 and 61-120 amino acids) and find that they can fold into native conformations independently. It is also found that their folding behaviors are very similar to other three-helix bundles. This suggests that this protein may be... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2627500 Wed, 24 Jun 2009 23:00:00 +0100 2627500 http://www.medworm.com/index.php?rid=2627499&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19616478%26dopt%3DAbstract Authors: Nicolau DV, Armitage JP, Maini PK E. coli does chemotaxis by performing a biased random walk composed of alternating periods of swimming (runs) and reorientations (tumbles). Tumbles are typically modelled as complete directional randomisations but it is known that in wild type E. coli, successive run directions are actually weakly correlated, with a mean directional difference of approximately 63 degrees . We recently presented a model of the evolution of chemotactic swimming strategies in bacteria which is able to quantitatively reproduce the emergence of this correlation. The agreement between model and experiments suggests that directional persistence may serve some function, a hypothesis supported by the results of an earlier model. Here we investigate the effect of persis... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2627499 Wed, 24 Jun 2009 23:00:00 +0100 2627499 http://www.medworm.com/index.php?rid=2580601&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19577519%26dopt%3DAbstract Authors: Scarle S In the arsenal of tools that a computational modeller can bring to bare on the study of cardiac arrhythmias, the most widely used and arguably the most successful is that of an excitable medium, a special case of a reaction-diffusion model. These are used to simulate the internal chemical reactions of a cardiac cell and the diffusion of their membrane voltages. Via a number of different methodologies it has previously been shown that reaction-diffusion systems are at multiple levels Turing complete. That is, they are capable of computation in the same manner as a universal Turing machine. However, all such computational systems are subject to a limitation known as the Halting problem. By constructing a universal logic gate using a cardiac cell model, we highlight how ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2580601 Wed, 10 Jun 2009 23:00:00 +0100 2580601 http://www.medworm.com/index.php?rid=2473450&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19395315%26dopt%3DAbstract Authors: Shelenkov A, Korotkov E In this paper, the notion of "regularity" is introduced to describe the structural features of DNA sequences. This notion expands the "latent periodicity" term. The novel method for revealing regularity based on the runs test is described. The search of regular sequences in eukaryotic promoters has shown that more than 60% of them possess a regularity property on statistically significant level. Possible biological functions of regularity are discussed together with the possibility of using this characteristic for performing promoter annotation. PMID: 19395315 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473450 Mon, 01 Jun 2009 04:00:00 +0100 2473450 http://www.medworm.com/index.php?rid=2473448&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19414282%26dopt%3DAbstract In this study a hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed an adaptive partitioning strategy in which processes with high frequency are simulated with deterministic rate-based equations, and those with low frequency using the exact stochastic algorithm of Gillespie. Therefore the stochastic behavior of cellular pathways is preserved while being able to apply it to large populations of molecules. We describe our method and demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetics with two steady states and second, a compartmental model of the postsynaptic spine head for studying the dynamics of Ca+2 and NMDA receptors. PMID: 19414282 [PubMed... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473448 Mon, 01 Jun 2009 04:00:00 +0100 2473448 http://www.medworm.com/index.php?rid=2473446&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19464954%26dopt%3DAbstract Authors: Furman DP, Bukharina TA Macrochaetes (large bristles), functioning as mechanoreceptors, are located in an orderly fashion on the drosophila head and body forming a species-specific bristle pattern. A simple organization of each bristle organ, comprising only four specialized cells, and conservation of bristle pattern make macrochaetes a convenient model for studying the development patterns of spatial structures with a fixed number of elements at certain positions and the mechanisms of cell differentiation. In this work, we systematize the experimental data on the main genes and their products that are involved in the control of proneural clusters in the ectoderm of imaginal discs and determination of the sensory organ precursor (SOP) cell within the proneural clusters. The co... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473446 Mon, 01 Jun 2009 04:00:00 +0100 2473446 http://www.medworm.com/index.php?rid=2473444&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19473879%26dopt%3DAbstract Authors: Jain P, Garibaldi JM, Hirst JD We explore automation of protein structural classification using supervised machine learning methods on a set of 11,360 pairs of protein domains (up to 35% sequence identity) consisting of three secondary structure elements. Fifteen algorithms from five categories of supervised algorithms are evaluated for their ability to learn for a pair of protein domains, the deepest common structural level within the SCOP hierarchy, given a one-dimensional representation of the domain structures. This representation encapsulates evolutionary information in terms of sequence identity and structural information characterising the secondary structure elements and lengths of the respective domains. The evaluation is performed in two steps, first selecting the be... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473444 Mon, 01 Jun 2009 04:00:00 +0100 2473444 http://www.medworm.com/index.php?rid=2473442&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19473880%26dopt%3DAbstract Authors: Singh TR, Pardasani KR Recoding events occur in competition with standard readout of the transcript, and are site-specific. Recoding is the reprogramming of mRNA translation by localized alterations in the standard translational rules. Frame-shifting is one class of recoding and defined as protein translations that start not at the first, but either at the second (+1 frame-shift) or the third (-1 frame-shift) nucleotide of the codon. Coding sequences lack stop codons, but frame-shifted sequences contain many stop codons, termed off-frame stops or hidden stops. These hidden stops terminate frame-shifted translation, potentially decreasing energy, and resource waste on non-functional proteins. Our results support this putative ancient adaptive event for the selection of codons t... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473442 Mon, 01 Jun 2009 04:00:00 +0100 2473442 http://www.medworm.com/index.php?rid=2473441&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19477686%26dopt%3DAbstract Authors: Vishnepolsky B, Pirtskhalava M The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473441 Mon, 01 Jun 2009 04:00:00 +0100 2473441 http://www.medworm.com/index.php?rid=2473439&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19477687%26dopt%3DAbstract Authors: Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt D, Przybytek J, Swiercz A, Szajkowski L Recently, 454 Life Sciences Corporation proposed a new biochemical approach to DNA sequencing (the 454 sequencing). It is based on the pyrosequencing protocol. The 454 sequencing aims to give reliable output at a low cost and in a short time. The produced sequences are shorter than reads produced by classical methods. Our paper proposes a new DNA assembly algorithm which deals well with such data and outperforms other assembly algorithms used in practice. The constructed SR-ASM algorithm is a heuristic method based on a graph model, the graph being a modified DNA graph proposed for DNA sequencing by hybridization procedure. Other new features of the assembly algor... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2473439 Mon, 01 Jun 2009 04:00:00 +0100 2473439 http://www.medworm.com/index.php?rid=2249308&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19266626%26dopt%3DAbstract Authors: Zuk T, Rakowski F, Radomski JP The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results of recent experiments, which involved infecting guinea pigs with influenza at various temperatures and relative air humidity levels. The wide range of transmission rates in those experiments reflects the ensemble-independent phenomena. The correlation between most of our simulations and the experimental results is satisfactory. For several different conditions, we obtained transmissibility value... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2249308 Sun, 08 Mar 2009 22:30:49 +0100 2249308 http://www.medworm.com/index.php?rid=2190716&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19217349%26dopt%3DAbstract Authors: Green RC, Thumser AE, Povey D, Saldanha JW, Potter BS, Palmer RA, Howlin BJ Recently published X-ray structures of three common forms, A, B and C, of oligomycin, including absolute configurations, are investigated to examine their binding to ATP Synthase. The X-ray studies reveal regions with differences in three-dimensional structure and hydrogen bonding propensity between the oligomycins, which may be associated with their potential to bind to sites on ATP Synthase. Computational docking studies carried out using MOE with the X-ray structures and an homology model of the F(O) domain of ATP Synthase from Escherichia coli, are used to derive an induced fit pocket. Docking of all oligomycins to this pocket indicate that the B and C forms bind more tightly than the A form. Consi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2190716 Mon, 19 Jan 2009 05:00:00 +0100 2190716 http://www.medworm.com/index.php?rid=2182707&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19211306%26dopt%3DAbstract This study obtains a near-optimal solution of primer sets that can be placed in as few test tubes as possible for one multiplex PCR experiment. RESULTS: Homo sapiens ribosomal protein L5, Homo sapiens xylosyltransferase I, and Bacteriophage T4 gene product 11 were used as test examples to verify efficacy of the proposed algorithm. In addition, the designed primers of Homo sapiens ribosomal protein L5 cDNA were applied in multiplex PCR experiments. A total of 48 forward primers and one reverse primer were designed and used to duplicate N-terminal truncated mutants of different lengths from the protein. The primers were classified into eight tube groups (i.e., test tubes) held within the same temperature range (53-57 degrees C), and the validity of the PCR products were verified using polyac... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2182707 Thu, 15 Jan 2009 05:00:00 +0100 2182707 http://www.medworm.com/index.php?rid=2156571&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19186108%26dopt%3DAbstract Authors: Babakhani A, Talley TT, Taylor P, McCammon JA The nicotinic acetylcholine receptor (nAChR) is a member of the ligand-gated ion channel family and is implicated in many neurological events. Yet, the receptor is difficult to target without high-resolution structures. In contrast, the structure of the acetylcholine binding protein (AChBP) has been solved to high resolution, and it serves as a surrogate structure of the extra-cellular domain in nAChR. Here we conduct a virtual screening study of the AChBP using the relaxed-complex method, which involves a combination of molecular dynamics simulations (to achieve receptor structures) and ligand docking. The library screened through comes from the National Cancer Institute, and its ligands show great potential for binding AChBP in v... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2156571 Thu, 08 Jan 2009 05:00:00 +0100 2156571 http://www.medworm.com/index.php?rid=2121852&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19152793%26dopt%3DAbstract We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html. PMID: 19152793 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2121852 Sat, 06 Dec 2008 05:00:00 +0100 2121852 http://www.medworm.com/index.php?rid=2061102&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19097944%26dopt%3DAbstract Authors: Zhang R Recently, Elhaik et al. [Elhaik, E., Graur, D., Josic, K., 2008. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences. Comp. Biol. Chem. 32, 147] commented on the genome order index, which is defined as S=a(2)+c(2)+g(2)+t(2) where a, c, g and t denote corresponding base frequencies. They claimed that (1) "S<1/3 is in fact a mathematical property that is always true", and (2) "S is strictly equivalent to and derivable from the Shannon H function". The first claim is apparently wrong: for instance, when a=c=0.5, g=t=0, S=0.5>1/3. The second claim is also incorrect because S and H are different special cases of the alpha-order entropy, having different functional forms that are neither strictly derivable from nor equ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=2061102 Fri, 14 Nov 2008 05:00:00 +0100 2061102 http://www.medworm.com/index.php?rid=1870921&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18845483%26dopt%3DAbstract Authors: Maugini E, Tronelli D, Bossa F, Pascarella S Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophilic homologs. Comparative studies were useful in the identification of a few recurrent themes which the evolution ut... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1870921 Sun, 31 Aug 2008 04:00:00 +0100 1870921 http://www.medworm.com/index.php?rid=1829230&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18815073%26dopt%3DAbstract Authors: Tsai KN, Lin SH, Shih SR, Lai JS, Chen CM Splice site prediction on an RNA virus has two potential difficulties seriously degrading the performance of most conventional splice site predictors. One is a limited number of strains available for a virus species and the other is the diversified sequence patterns around the splice sites caused by the high mutation frequency. To overcome these two difficulties, a new algorithm called Genomic Splice Site Prediction (GSSP) algorithm, was proposed for splice site prediction of RNA viruses. The key idea of the GSSP algorithm was to characterize the interdependency among the nucleotides and base positions based on the eigen-patterns. Identified by a sequence pattern mining technique, each eigen-pattern specified a unique composition of th... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1829230 Wed, 20 Aug 2008 04:00:00 +0100 1829230 http://www.medworm.com/index.php?rid=1829231&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18815072%26dopt%3DAbstract Authors: An J, Chen YP Microarray data provides quantitative information about the transcription profile of cells. To analyze microarray datasets, methodology of machine learning has increasingly attracted bioinformatics researchers. Some approaches of machine learning are widely used to classify and mine biological datasets. However, many gene expression datasets are extremely high dimensionality, traditional machine learning methods cannot be applied effectively and efficiently. This paper proposes a robust algorithm to find out rule groups to classify gene expression datasets. Unlike the most classification algorithms, which select dimensions (genes) heuristically to form rules groups to identify classes such as cancerous and normal tissues, our algorithm guarantees finding out best... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1829231 Thu, 14 Aug 2008 04:00:00 +0100 1829231 http://www.medworm.com/index.php?rid=1798252&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18789768%26dopt%3DAbstract Authors: Teramoto R Alzheimer's disease (AD) is the most common form of dementia and leads to irreversible neurogenerative damage of the brain. However, the current diagnostic tools have poor sensitivity, especially for the early stages of AD and do not allow for diagnosis until AD has lead to irreversible brain damage. Therefore, it is crucial that AD is detected as early as possible. Although it is very hard, laborious and time-consuming to gather many AD and non-AD labeled samples, gathering unlabeled samples is easier than labeled samples. Since standard learning algorithms learn a diagnosis model from labeled samples only, they require many labeled samples and do not work well when the number of training samples is small. Therefore, it is very desirable to develop a predictive lea... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1798252 Fri, 08 Aug 2008 04:00:00 +0100 1798252 http://www.medworm.com/index.php?rid=1798250&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18789770%26dopt%3DAbstract Authors: Chang HW, Yang CH, Ho CH, Wen CH, Chuang LY Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SNP combinations with genotypes called "SNP barcode". DBPSO are applied to generate SNP barcode, which computes the maximal difference of occurrence between the case and control groups, to predict disease susceptibility such as osteoporosis. Different SNP barcode patterns may occur several times in either low or high bone mineral density (BMD) groups. Our results showed that a DBPSO can effectively identify a specific SNP ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1798250 Fri, 08 Aug 2008 04:00:00 +0100 1798250 http://www.medworm.com/index.php?rid=1798251&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18789769%26dopt%3DAbstract Authors: Hosseini SR, Sadeghi M, Pezeshk H, Eslahchi C, Habibi M The automatic assignment of secondary structure from three-dimensional atomic coordinates of proteins is an essential step for the analysis and modeling of protein structures. So different methods based on different criteria have been designed to perform this task. We introduce a new method for protein secondary structure assignment based solely on C(alpha) coordinates. We introduce four certain relations between C(alpha) three-dimensional coordinates of consecutive residues, each of which applies to one of the four regular secondary structure categories: alpha-helix, 3(10)-helix, pi-helix and beta-strand. In our approach, the deviation of the C(alpha) coordinates of each residue from each relation is calculated. Based on... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1798251 Wed, 06 Aug 2008 04:00:00 +0100 1798251 http://www.medworm.com/index.php?rid=1786038&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18782681%26dopt%3DAbstract Authors: Chen H, Huang Y, Xiao Y Accurate identifications of internal symmetric substructures of proteins are needed in protein evolution study and protein design. To overcome the difficulties met by previous methods, here we propose a simple quantitative one by using a similarity matrix plus Pearson's correlation analysis. The distance root-mean-square deviation (dRMSD) is used to measure the similarity of two substructures in a protein. We applied this method to the proteins of the beta-propeller, jelly roll, and beta-trefoil families and the results show that this method cannot only detect the internal repetitive structures in proteins effectively, but also can identify their locations easily. PMID: 18782681 [PubMed - as supplied by publisher] (Source: Computational Biology and ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1786038 Sun, 03 Aug 2008 04:00:00 +0100 1786038 http://www.medworm.com/index.php?rid=1754821&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760970%26dopt%3DAbstract In this study, we focused on computational search of novel miRNA homologs in chimpanzee. We have searched and analyzed the chimp homologs of the human pre-miRNA and mature miRNA sequences. Based on a homology search of the chimpanzee genome with human miRNA precursor sequences as queries, we identified 639 chimp miRNA genes, including 529 novel chimp miRNAs. 91.8% of chimp mature miRNAs and 60.3% of precursors are 100% identical to their human orthologs. The pre-miRNA secondary structures, miRNA families, and clusters are also highly conserved. We also found certain sequence differences in pre-miRNAs and even mature miRNAs that occurred after the divergence of the two species. Some of these differences (especially in mature miRNAs) could have caused species-specific changes in the expressi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1754821 Sat, 26 Jul 2008 04:00:00 +0100 1754821 http://www.medworm.com/index.php?rid=1754822&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760969%26dopt%3DAbstract Authors: Mamedov TG, Pienaar E, Whitney SE, Termaat JR, Carvill G, Goliath R, Subramanian A, Viljoen HJ A theoretical analysis is presented with experimental confirmation to conclusively demonstrate the critical role that annealing plays in efficient PCR amplification of GC-rich templates. The analysis is focused on the annealing of primers at alternative binding sites (competitive annealing) and the main result is a quantitative expression of the efficiency (eta) of annealing as a function of temperature (T(A)), annealing period (t(A)), and template composition. The optimal efficiency lies in a narrow region of T(A) and t(A) for GC-rich templates and a much broader region for normal GC templates. To confirm the theoretical findings, the following genes have been PCR amplified from hum... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1754822 Fri, 25 Jul 2008 04:00:00 +0100 1754822 http://www.medworm.com/index.php?rid=1746406&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18755632%26dopt%3DAbstract In this study, we intend to utilize room temperature simulation to study the stability of the modeling structure for GIFQINS. The results suggest that the hexamer of GIFQINS is highly stable and consistent with the prediction of Eisenberg. Furthermore, high-temperature molecular dynamics simulation in explicit water is used to study its aggregation mechanisms. The important findings from this work are (a) dimer is not thermodynamically stable state, (b) dissolution of the fibrils is more difficult than aggregation, (c) tetramer (2-2) is the intermediate state and (d) two transition states are corresponding to trimer (2-1) and pentamer (3-2). This is the first time to suggest the tetramer (2-2) as intermediate state with kinetics analysis and can shed light on possible mechanisms of aggrega... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746406 Fri, 25 Jul 2008 04:00:00 +0100 1746406 http://www.medworm.com/index.php?rid=1746412&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18722814%26dopt%3DAbstract Authors: Webb-Robertson BJ, Oehmen CS, Shah AR Due to the exponential growth of sequenced genomes, the need to quickly provide accurate annotation for existing and new sequences is paramount to facilitate biological research. Current sequence comparison approaches fail to detect homologous relationships when sequence similarity is low. Support vector machine (SVM) algorithms approach this problem by transforming all proteins into a feature space of equal dimension based on protein properties, such as sequence similarity scores against a basis set of proteins or motifs. This multivariate representation of the protein space is then used to build a classifier specific to a pre-defined protein family. However, this approach is not well suited to large-scale annotation. We have developed a ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746412 Wed, 16 Jul 2008 04:00:00 +0100 1746412 http://www.medworm.com/index.php?rid=1746411&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18722815%26dopt%3DAbstract Authors: Leng C Gene expression data sets hold the promise to provide cancer diagnosis on the molecular level. However, using all the gene profiles for diagnosis may be suboptimal. Detection of the molecular signatures not only reduces the number of genes needed for discrimination purposes, but may elucidate the roles they play in the biological processes. Therefore, a central part of diagnosis is to detect a small set of tumor biomarkers which can be used for accurate multiclass cancer classification. This task calls for effective multiclass classifiers with built-in biomarker selection mechanism. We propose the sparse optimal scoring (SOS) method for multiclass cancer characterization. SOS is a simple prototype classifier based on linear discriminant analysis, in which predictive bio... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746411 Wed, 16 Jul 2008 04:00:00 +0100 1746411 http://www.medworm.com/index.php?rid=1746409&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18723399%26dopt%3DAbstract Authors: Kim S, Choi M, Cho KH MicroRNAs (miRNAs) play an important role in gene regulatory networks by inhibiting the expression of target mRNAs. There is a growing interest in identifying the relationship between miRNAs and their target mRNAs. Various experimental studies have been carried out to discover miRNAs involved in cancer and to identify their target genes. At the same time, a large volume of miRNA and mRNA expression profiles have become available owing to the development of high-throughput measurement technologies. So, there is now a pressing need to develop a computational method by which we can identify the target mRNAs of given miRNAs from such massive expression data sets. In this respect, we propose an effective linear model based identification method to unravel the ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746409 Wed, 16 Jul 2008 04:00:00 +0100 1746409 http://www.medworm.com/index.php?rid=1746408&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18723400%26dopt%3DAbstract Authors: Nasibov E, Kandemir-Cavas C Optimally weighted fuzzy k-nearest neighbors (OWFKNN) algorithm has been used to predict proteins' subcellular locations based on their amino acid composition, in this paper. The datasets used consists of two species which are 997 prokaryotic and 2427 eukaryotic protein sequences. The overall prediction accuracy achieved is about 88.5% for prokaryotic sequences and 86.2% for eukaryotic sequences in a jackknife test. Compared to other algorithms developed for the prediction of protein subcellular location, OWFKNN gives very satisfying results. Therefore, OWFKNN can be used as an alternative method to predict protein localization. PMID: 18723400 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746408 Wed, 16 Jul 2008 04:00:00 +0100 1746408 http://www.medworm.com/index.php?rid=1746407&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18755631%26dopt%3DAbstract Authors: Bondavalli C, Favilla S, Bodini A Natural disturbance or human perturbation act upon ecosystems by changing some dynamical parameters of one or more species. Foreseeing these modifications is necessary before embarking on an intervention: predictions may help to assess management options and define hypothesis for interventions. Models become valuable tools for studying and making predictions only when they capture types of interactions and their magnitude. Quantitative models are more precise and specific about a system, but require a large effort in model construction. Because of this very often ecological systems remain only partially specified and one possible approach to their description and analysis comes from qualitative modelling. Qualitative models yield predictions a... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746407 Wed, 16 Jul 2008 04:00:00 +0100 1746407 http://www.medworm.com/index.php?rid=1746410&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18723398%26dopt%3DAbstract Authors: Zhang W, Luo Y, Gong X, Zeng W, Li S MicroRNAs (miRNAs) are a new family of small RNA molecules known in animals and plants, whose conservation among species suggests that they bear conserved biological functions. So far, little is known about miRNA in Solanum tuberosum species. Using previously known miRNAs from Arabidopsis, rice and other plant species against expressed sequence tags (ESTs), genomic survey sequence (GSS) and nucleotide databases, we identified 48 potential miRNAs in S. tuberosum. These potato miRNAs may regulate 186 potential targets, which are involved in floral, leaf, root, and stem development, signal transduction, metabolism pathways, and stress responses. To validate the prediction of miRNAs in potato, we performed a RT-PCR analysis and found that potat... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746410 Tue, 15 Jul 2008 04:00:00 +0100 1746410 http://www.medworm.com/index.php?rid=1746405&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18755633%26dopt%3DAbstract Authors: Song JJ, Deng W, Lee HJ, Kwon D Classification problems have received considerable attention in biological and medical applications. In particular, classification methods combining to microarray technology play an important role in diagnosing and predicting disease, such as cancer, in medical research. Primary objective in classification is to build an optimal classifier based on the training sample in order to predict unknown class in the test sample. In this paper, we propose a unified approach for optimal gene classification with conjunction with functional principal component analysis (FPCA) in functional data analysis (FNDA) framework to classify time-course gene expression profiles based on information from the patterns. To derive an optimal classifier in FNDA, we also p... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1746405 Tue, 15 Jul 2008 04:00:00 +0100 1746405 http://www.medworm.com/index.php?rid=1717272&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18706866%26dopt%3DAbstract Authors: Rodrigues AM, Almeida AC, Infantosi AF, Teixeira HZ, Duarte MA K(+) has been appointed as the main physiological inhibitor of the palytoxin (PTX) effect on the Na(+)/K(+) pump. This toxin acts opening monovalent cationic channels through the Na(+)/K(+) pump. We investigate, by means of computational modeling, the kinetic mechanisms related with K(+) interacting with the complex PTX-Na(+)/K(+) pump. First, a reaction model, with structure similar to Albers-Post model, describing the functional cycle of the pump, was proposed for describing K(+) interference on the complex PTX-Na(+)/K(+) pump in the presence of intracellular ATP. A mathematic model was derived from the reaction model and it was possible to solve numerically the associated differential equations and to simulate e... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1717272 Tue, 15 Jul 2008 04:00:00 +0100 1717272 http://www.medworm.com/index.php?rid=1709343&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18701351%26dopt%3DAbstract Authors: Khoshmanesh K, Kouzani AZ, Nahavandi S, Baratchi S, Kanwar JR Engineering contributions have played an important role in the rise and evolution of cellular biology. Engineering technologies have helped biologists to explore the living organisms at cellular and molecular levels, and have created new opportunities to tackle the unsolved biological problems. There is now a growing demand to further expand the role of engineering in cellular biology research. For an engineer to play an effective role in cellular biology, the first essential step is to understand the cells and their components. However, the stumbling block of this step is to comprehend the information given in the cellular biology literature because it best suits the readers with a biological background. This paper... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1709343 Tue, 15 Jul 2008 04:00:00 +0100 1709343 http://www.medworm.com/index.php?rid=1709342&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18703385%26dopt%3DAbstract Authors: Towsey M, Timms P, Hogan J, Mathews SA Due to degeneracy of the observed binding sites, the in silico prediction of bacterial sigma(70)-like promoters remains a challenging problem. A large number of sigma(70)-like promoters has been biologically identified in only two species, Escherichia coli and Bacillus subtilis. In this paper we investigate the issues that arise when searching for promoters in other species using an ensemble of SVM classifiers trained on E. coli promoters. DNA sequences are represented using a tagged mismatch string kernel. The major benefit of our approach is that it does not require a prior definition of the typical -35 and -10 hexamers. This gives the SVM classifiers the freedom to discover other features relevant to the prediction of promoters. We use... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1709342 Tue, 15 Jul 2008 04:00:00 +0100 1709342 http://www.medworm.com/index.php?rid=1709344&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18701350%26dopt%3DAbstract Authors: Barea F, Tessaro S, Bonatto D Bacterial and eukaryotic RecQ helicases comprise a family of homologous proteins necessary for maintaining genomic integrity during the cell cycle and DNA repair. There is one known bacterial RecQ helicase, and five eukaryotic RecQ helicases that have been described: RecQ1p, RecQ4p, RecQ5p, Bloom, and Werner. While the biochemical functions of Bloom and Werner helicases are well understood, the same is not true for RecQ4p helicase. RecQ4p mutations lead to pathologies like Rothmund-Thompson syndrome (RTS), RAPADILINO, and Baller-Gerold syndrome (BGS). Until now, RecQ4p helicases had only been described in metazoans, and their presence in organisms like fungi and plants were not known. Thus far only one RecQ-homologous protein (Sgs1p), similar to B... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1709344 Fri, 11 Jul 2008 04:00:00 +0100 1709344 http://www.medworm.com/index.php?rid=1692236&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18684672%26dopt%3DAbstract Authors: Surmeli D, Ratmann O, Mewes HW, Tetko IV Pairwise comparison of sequence data is intensively used for automated functional protein annotation, while graphical models emerge as promising candidates for an integration of various heterogeneous features. We designed a model, termed hRMN that integrates different genomic features and implemented a variant of belief propagation for functional annotation transfer. hRMN allows the assignment of multiple functional categories while avoiding common problems in annotation transfer from heterogeneous datasets, such as an independency of the investigated datasets. We benchmarked this system with large-scale annotation transfer (based on the MIPS FunCat ontology) to proteins of the prokaryotes Bacillus subtilis, Helicobacter pylori, Listeri... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1692236 Thu, 03 Jul 2008 04:00:00 +0100 1692236 http://www.medworm.com/index.php?rid=1603146&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18602867%26dopt%3DAbstract Authors: Tatulian SA Accurate description of helices, including curvature and bending, and determination of interhelical angles are essential for analysis of the three-dimensional fold and functionally important conformational changes in helical proteins. Here, a new computational method is presented that allows determination of angles between any helical stretches, the radius of curvature of curved helices, bending angle of bent helices, as well as symmetry relations within the protein molecule, using main chain atom coordinates. The method has been applied to describe changes in interhelical angles in calmodulin upon interaction with a target peptide, which reveals the conformational changes at a higher precision. Because subtle changes in helix-to-helix packing and interhelical angl... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1603146 Thu, 03 Jul 2008 04:00:00 +0100 1603146 http://www.medworm.com/index.php?rid=1469788&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18502690%26dopt%3DAbstract Authors: Du Z, Wang Y, Ji Z Microarray technology has been widely applied in study of measuring gene expression levels for thousands of genes simultaneously. Gene cluster analysis is found useful for discovering the function of gene because co-expressed genes are likely to share the same biological function. K-means is one of well-known clustering methods. However, it is sensitive to the selection of an initial clustering and easily becoming trapped in a local minimum. Particle-pair optimizer (PPO) is a variation on the traditional particle swarm optimization (PSO) algorithm, which is stochastic particle-pair based optimization technique that can be applied to a wide range of problems. In this paper we bridges PPO and K-means within the algorithm PK-means for the first time. Our result... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1469788 Fri, 23 May 2008 04:00:00 +0100 1469788 http://www.medworm.com/index.php?rid=1466143&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18499525%26dopt%3DAbstract Authors: Sandmann W Since inherent randomness in chemically reacting systems is evident, stochastic modeling and simulation are exceedingly important for investigating complex biological networks. Within the most common stochastic approach a network is modeled by a continuous-time Markov chain governed by the chemical master equation. We show how the continuous-time Markov chain can be converted to a stochastically identical discrete-time Markov chain and obtain a discrete-time version of the chemical master equation. Simulating the discrete-time Markov chain is equivalent to the Gillespie algorithm but requires less effort in that it eliminates the generation of exponential random variables. Thus, exactness as possessed by the Gillespie algorithm is preserved while the simulation can ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1466143 Thu, 10 Apr 2008 04:00:00 +0100 1466143 http://www.medworm.com/index.php?rid=1439695&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18468491%26dopt%3DAbstract Authors: Takasaki S In this paper we examined the relations between three classes of people (96 Japanese centenarians, 96 Japanese Alzheimer's disease (AD) patients and 96 Japanese Parkinson's disease (PD) patients) and their mitochondrial single nucleotide polymorphism (mtSNP) frequencies at individual mitochondrial DNA (mtDNA) positions of the entire mt-genome by using the radial basis function (RBF) networks. As a result, we got new findings of mtSNPs for representing characteristics of individual classes. These mtSNPs show distinct differences for three classes of people. That is, individual classes of people are characterized by unique mtSNPs. Interestingly, Japanese centenarians are closely associated with haplogroup D4, Japanese AD patients with haplogroup G2a, and Japanese PD p... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1439695 Tue, 08 Apr 2008 04:00:00 +0100 1439695 http://www.medworm.com/index.php?rid=1439694&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18472302%26dopt%3DAbstract Authors: Khaladkar M, Patel V, Bellofatto V, Wilusz J, Wang JT Constrained sequence alignment has been studied extensively in the past. Different forms of constraints have been investigated, where a constraint can be a subsequence, a regular expression, or a probability matrix of symbols and positions. However, constrained structural alignment has been investigated to a much lesser extent. In this paper, we present an efficient method for constrained structural alignment and apply the method to detecting conserved secondary structures, or structural motifs, in a set of RNA molecules. The proposed method combines both sequence and structural information of RNAs to find an optimal local alignment between two RNA secondary structures, one of which is a query and the other is a subject str... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1439694 Tue, 08 Apr 2008 04:00:00 +0100 1439694 http://www.medworm.com/index.php?rid=1433809&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18467179%26dopt%3DAbstract Authors: Zhou W, Peng X, Yan Z, Wang Y Some biochemical processes do not occur instantaneously but have considerably delays associated with them. In the existed methods which solve these chemically reacting systems with delays, averaging over a great deal of simulations is needed for reliable statistical characters. Here we present an accelerating approach, called the "Delay Final All Possible Steps" (DFAPS) approach, which does not alter the course of stochastic simulation, but reduces the required running times. Numerical simulation results indicate that the proposed method can be applied to a wide range of chemically reacting systems with delays and obtain a significant improvement on efficiency and accuracy over the existed methods. PMID: 18467179 [PubMed - as supplied by publi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1433809 Mon, 07 Apr 2008 04:00:00 +0100 1433809 http://www.medworm.com/index.php?rid=1292310&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18313988%26dopt%3DAbstract Authors: Budhachandra Kh, Brojen Singh RK, Menon GI Microtubules perform a variety of functions which lead to the complex regulation of intracellular transport and cell division. However, the regulation of microtubule growth is not clearly known. Based on a recent experimental finding, we explore the possibility of spatial regulation of microtubule growth by stathmin-tubulin interaction gradients. Computer simulation of the model with stathmin-tubulin interaction gradients gave regulated growth as seen in experiments. In future, the stathmin-tubulin interaction gradients can be made dynamic and its impact on the microtubule growth can be explored. PMID: 18313988 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1292310 Tue, 11 Mar 2008 08:14:00 +0100 1292310 http://www.medworm.com/index.php?rid=1139868&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18165158%26dopt%3DAbstract Authors: Zhou D, Li S, Wen J, Gong X, Xu L, Luo Y By computational analyses, we identified 357 miRNA candidates from Canis familiaris genome, among which 300 are homology of characterized human miRNAs, the remains are not reported in any other animal. Of the 357 miRNA genes, 142 are organized into 53 clusters, and two clusters locate in the paternally imprinted region. These dog miRNAs may regulate more than 800 possible targets, which are involved in a wide range of cellular processes. Remarkably, miR-186 resides in the eighth intron of its target gene in the same orientation, suggesting a feedback regulation of miRNA on its host gene. PMID: 18165158 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1139868 Thu, 10 Jan 2008 00:49:10 +0100 1139868 http://www.medworm.com/index.php?rid=1139867&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18165159%26dopt%3DAbstract Authors: Wu J, Tan Y, Deng H, Zhu D It is argued that both the degree-rank function r=f(d), which describes the relationship between the degree d and the rank r of a degree sequence, and the degree distribution P(k), which describes the probability that a randomly chosen vertex has degree k, are important statistical properties to characterize protein-protein interaction (PPI) networks, both rank-degree plot and frequency-degree plot are reliable tools to analyze PPI networks. An exact mathematical relationship between degree-rank functions and degree distributions of PPI networks is derived. It is demonstrated that a power law degree distribution is equivalent to a power law degree-rank function only if scaling exponent is greater than 2. The puzzle that the degree distributions of so... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1139867 Thu, 10 Jan 2008 00:49:08 +0100 1139867 http://www.medworm.com/index.php?rid=1101516&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18082453%26dopt%3DAbstract Authors: Bolanos-Garcia VM PMID: 18082453 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1101516 Wed, 24 Oct 2007 04:00:00 +0100 1101516 http://www.medworm.com/index.php?rid=1101515&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18082454%26dopt%3DAbstract Authors: Ng KL, Huang CH, Liu HC, Liu HC The domain combination pair approach is employed to derive putative protein domain-domain interactions (DDI) from the protein-protein interactions (PPI) database DIP. The results of putative DDI are computed for seven species. To determine the prediction performance, putative DDI results are compared with that of the database InterDom, where an average matching ratio of about 76% can be achieved. Several real PPI pathways are reconstructed based on the predicted DDI results. It is found that the pathways could be reconstructed with reasonable accuracy. Furthermore, a novel quantity, so called AP-order index, is introduced to predict the regulatory order for six PPI pathways. It is found that the AP-order index is a very reliable parameter to det... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=1101515 Mon, 22 Oct 2007 04:00:00 +0100 1101515 http://www.medworm.com/index.php?rid=947983&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17920334%26dopt%3DAbstract Authors: Verboven S, Branden KV, Goos P As missing values are often encountered in gene expression data, many imputation methods have been developed to substitute these unknown values with estimated values. Despite the presence of many imputation methods, these available techniques have some disadvantages. Some imputation techniques constrain the imputation of missing values to a limited set of genes, whereas other imputation methods optimise a more global criterion whereby the computation time of the method becomes infeasible. Others might be fast but inaccurate. Therefore in this paper a new, fast and accurate estimation procedure, called SEQimpute, is proposed. By introducing the idea of minimisation of a statistical distance rather than a Euclidean distance the method is intrinsica... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=947983 Mon, 01 Oct 2007 04:00:00 +0100 947983 http://www.medworm.com/index.php?rid=903448&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17888742%26dopt%3DAbstract Authors: Costantini S, Colonna G, Facchiano AM PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the diffe... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903448 Wed, 22 Aug 2007 04:00:00 +0100 903448 http://www.medworm.com/index.php?rid=903447&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17888743%26dopt%3DAbstract Authors: Zarei R, Arab S, Sadeghi M Prediction of protein accessibility from sequence, as prediction of protein secondary structure is an intermediate step for predicting structures and consequently functions of proteins. Most of the currently used methods are based on single residue prediction, either by statistical means or evolutionary information, and accessibility state of central residue in a window predicted. By expansion of databases of proteins with known 3D structures, we extracted information of pairwise residue types and conformational states of pairs simultaneously. For solving the problem of ambiguity in state prediction by one residue window sliding, we used dynamic programming algorithm to find the path with maximum score. The three state overall per-residue accuracy, Q... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903447 Sun, 19 Aug 2007 04:00:00 +0100 903447 http://www.medworm.com/index.php?rid=903446&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17889617%26dopt%3DAbstract Authors: Wang M, Chen Z, Cloutier S A Bayesian network (BN) is a knowledge representation formalism that has proven to be a promising tool for analyzing gene expression data. Several problems still restrict its successful applications. Typical gene expression databases contain measurements for thousands of genes and no more than several hundred samples, but most existing BNs learning algorithms do not scale more than a few hundred variables. Current methods result in poor quality BNs when applied in such high-dimensional datasets. We propose a hybrid constraint-based scored-searching method that is effective for learning gene networks from DNA microarray data. In the first phase of this method, a novel algorithm is used to generate a skeleton BN based on dependency analysis. Then the r... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903446 Sun, 19 Aug 2007 04:00:00 +0100 903446 http://www.medworm.com/index.php?rid=903444&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17890157%26dopt%3DAbstract Authors: He D, Zhou D, Zhou Y Finding transcription factors (TFs) to their target genes (TGs) is the first step to understand the transcriptional regulatory networks. Here we present a method which uses an enhanced Bayesian classifier to predict the TF-TG pairs in time-course expression data. Different from previous prediction models, the gene expression data is encoded by discrete values and the temporal feature is used in the enhanced Bayesian classifier. The enhanced Bayesian classifier is trained and tested on two groups of positive and negative samples by three-fold cross-validation and compared with other methods. As the prediction result is improved obviously, the enhanced Bayesian classifier represents a new perspective on studying the regulation relationships from gene express... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903444 Sun, 19 Aug 2007 04:00:00 +0100 903444 http://www.medworm.com/index.php?rid=903443&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17890158%26dopt%3DAbstract Authors: Chen K, Huang X Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNA... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903443 Fri, 17 Aug 2007 04:00:00 +0100 903443 http://www.medworm.com/index.php?rid=903442&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17890159%26dopt%3DAbstract We present an optimization-based inference scheme to unravel the functional interaction structure of biomolecular components within a cell. The regulatory network of a cell is inferred from the data obtained by perturbation of adjustable parameters or initial concentrations of specific components. It turns out that the identification procedure leads to a convex optimization problem with regularization as we have to achieve the sparsity of a network and also reflect any a priori information on the network structure. Since the convex optimization has been well studied for a long time, a variety of efficient algorithms were developed and many numerical solvers are freely available. In order to estimate time derivatives from discrete-time samples, a cubic spline fitting is incorporated into th... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903442 Fri, 17 Aug 2007 04:00:00 +0100 903442 http://www.medworm.com/index.php?rid=903445&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17889618%26dopt%3DAbstract Authors: Kim M, Baek S, Jung SH, Cho KH Motivated by the recent work on Escherichia coli bacteria clustering [Park, S., Wolanin, P.M., Yuzbashyan, E.A., Lin, H., Darnton, N.C., Stock, J.B., Silberzan, P., Austin, R., 2003. Proc. Natl. Acad. Sci. U.S.A. 100 (24), 13910], we have conducted a computer simulation of E. coli chemotaxis induced by a self-excreted attractant and investigated how bacteria clusters interact through a self-excreted attractant. By modeling the variation of tumbling frequency in the context of phosphorylation rate change, we have investigated the dependency of clustering behavior on the sensitivity of cells to the attractant. We have found that there exists an optimal sensitivity leading to bigger clusters and that the geometry surrounding the cells also plays an ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=903445 Mon, 06 Aug 2007 04:00:00 +0100 903445 http://www.medworm.com/index.php?rid=752915&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17644485%26dopt%3DAbstract Authors: Yoon S, Welsh WJ, Jung H, Yoo YD The calculation of contact-dependent secondary structure propensity (CSSP) has been reported to sensitively detect non-native beta-strand propensities in the core sequences of amyloidogenic proteins. Here we describe a noble energy-based CSSP method implemented on dual artificial neural networks that rapidly and accurately estimate the potential for the non-native secondary structure formation in local regions of protein sequences. In this method, we attempted to quantify long-range interaction patterns in diverse secondary structures by potential energy calculations and decomposition on a pairwise per-residue basis. The calculated energy parameters and seven-residue sequence information were used as inputs for artificial neural networks (ANNs)... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=752915 Sat, 16 Jun 2007 04:00:00 +0100 752915 http://www.medworm.com/index.php?rid=738980&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17631416%26dopt%3DAbstract Authors: Yap YL, Zhang XW, Smith D, Soong R, Hill J It is an accepted clinical practice to diagnose gastric cancer by using histological techniques on tissue obtained through endoscopic biopsy. However, the use of these techniques often results in difficulty distinguishing between benign and malignant growth due to the ambiguous nature of some of the morphological features observed. In order to improve this situation, public domain gene expression data has been analysed and a set of molecular gene expression signatures has been discovered that distinguishes between normal and malignant growth. In addition, a separate distinct gene expression signature has been identified that appears to aid in the prognosis and indicate survival rates of patients. It is proposed that the use of the mol... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=738980 Wed, 13 Jun 2007 04:00:00 +0100 738980 http://www.medworm.com/index.php?rid=738979&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17631419%26dopt%3DAbstract Authors: Song JJ, Lee HJ, Morris JS, Kang S Clustering of gene expression data collected across time is receiving growing attention in the biological literature since time-course experiments allow one to understand dynamic biological processes and identify genes governed by the same processes. It is believed that genes demonstrating similar expression profiles over time might give an informative insight into how underlying biological mechanisms work. In this paper, we propose a method based on functional data analysis (FNDA) to cluster time-dependent gene expression profiles. Consideration of clustering problems using the FNDA setting provides ways to take time dependency into account by using basis function expansion to describe the partially observed curves. We also discuss how to ch... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=738979 Sat, 02 Jun 2007 04:00:00 +0100 738979 http://www.medworm.com/index.php?rid=638380&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17499548%26dopt%3DAbstract Authors: Yu W, Liu J, Colangelo C, Gulcicek E, Zhao H Isotope-coded affinity tags (ICAT) is a labeling technique that provides insights into quantitative molecular changes. In this paper, we propose a new protocol to identify and analyze ICAT labeled peak pairs in high-resolution LC-MS data. Our major contributions are: (1) we use isotope distance constraint, ICAT distance constraint, and LC-span constraint to identify ICAT labeled peak pairs and (2) we propose to trigger tandem MS/MS scanning based on the ratio estimation value of identified ICAT peak pairs instead of the peak intensity values. Compared with current approaches that choose peaks with high intensity values for tandem MS/MS scanning, the new protocol can improve the scanning efficiency and accuracy. PMID: 17499548 [P... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638380 Sun, 27 May 2007 03:43:46 +0100 638380 http://www.medworm.com/index.php?rid=638379&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17499549%26dopt%3DAbstract Authors: Inouchi A, Shinohara S, Inoue H, Kita K, Itakura M We have identified novel over-represented and conserved motifs in the upstream regions of human and mouse miRNA stem-loop sequences by means of a new bioinformatic processing regimen. We observed sequence conservation -500bp upstream in 189 human and mouse miRNAs declining with increasing distance from their putative miRNA stem-loop origin. We also found relatively GC-rich regions having more than 50% of guanine+cytosine (G+C) content at about -30 and -170bp relative to human miRNA stem-loop sequence origin. To further identify specific sequence motifs that might be involved in the transcriptional regulation of miRNA precursors, we first searched 500bp upstream sequences of 194 non-redundant human miRNA stem-loop sequences for... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638379 Sun, 27 May 2007 03:43:46 +0100 638379 http://www.medworm.com/index.php?rid=638378&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17499550%26dopt%3DAbstract Authors: Gusnanto A, Tom B, Burns P, Macaulay I, Thijssen-Timmer DC, Tijssen MR, Langford C, Watkins N, Ouwehand W, Berzuini C, Dudbridge F Our ability to detect differentially expressed genes in a microarray experiment can be hampered when the number of biological samples of interest is limited. In this situation, we propose the use of information from self-self hybridizations to acuminate our inference of differential expression. A unified modelling strategy is developed to allow better estimation of the error variance. This principle is similar to the use of a pooled variance estimate in the two-sample t-test. The results from real dataset examples suggest that we can detect more genes that are differentially expressed in the combined models. Our simulation study provides evidence t... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638378 Sun, 27 May 2007 03:43:46 +0100 638378 http://www.medworm.com/index.php?rid=638377&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17499551%26dopt%3DAbstract Authors: Zhang GZ, Han K Inter-residue contact map is an important two-dimensional representation of protein spatial structure, and has much potential application in the area of understanding protein fold mechanism. In the present note, a 19-bit binary input encoding strategy, integrating with residue pair conformational features (possible residue pairwise, residue classification, secondary structure, sequence length, and sequence separation information), is proposed for the purpose of capturing mapping relationship of protein sequence. Simulation results on a set of 61 hepatitis C virus (HCV) retrieved from the protein data bank (PDB) demonstrate that the proposed encoding scheme could precisely capture conformational patterns within HCV protein sequence. This promising result could p... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638377 Sun, 27 May 2007 03:43:46 +0100 638377 http://www.medworm.com/index.php?rid=638376&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500034%26dopt%3DAbstract Authors: Altermark B, Thorvaldsen S, Moe E, Smalås AO, Willassen NP The periplasmic/extracellular bacterial enzyme endonuclease I was chosen as a model system to identify features that might be responsible for temperature- and salt adaptation. A statistical study of amino acid sequence properties belonging to endonuclease I enzymes from three mesophilic habitats (non-marine, brackish water and marine), and three marine temperature groups (psychrophile, intermediate and mesophile) has been conducted. Ten new endonuclease I genes have been sequenced in order to increase the sample size. A bioinformatical method of property dependent statistical analysis of alignments has been applied. To our knowledge this is the first time these methods have been used in order to investigate environmen... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638376 Sun, 27 May 2007 03:43:46 +0100 638376 http://www.medworm.com/index.php?rid=638375&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500035%26dopt%3DAbstract Authors: Costantini S, Colonna G, Facchiano AM In order to simulate the conformational changes occurring when a protein interacts with its receptor, we firstly evaluated the structural differences between the experimental unbound and bound conformations for selected proteins and created theoretical complexes by replacing, in each experimental complex, the protein-bound with the protein-unbound chain. The theoretical models were then subjected to additional modeling refinements to improve the side chain geometry. Comparing the theoretical and experimental complexes in term of structural and energetic factors is resulted that the refined theoretical complexes became more similar to the experimental ones. We applied the same procedure within an homology modeling experiment, using as templ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638375 Sun, 27 May 2007 03:43:46 +0100 638375 http://www.medworm.com/index.php?rid=638374&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500036%26dopt%3DAbstract Authors: Lu L, Qian Z, Cai YD, Li Y Classification for enzymes is a prerequisite for understanding their function. Here, an automatic enzyme identifier based on support vector machine (SVM) with feature vectors from protein functional domain composition was built to identify enzymes and further a classifier to classify enzymes into six different classes: oxidoreductase, transferase, hydrolase, lyase, isomerase and ligase. Jackknife cross-validation test was adopted to evaluate the performance of our classifier. The 86.03% success rate achieved for enzyme/non-enzyme identification and 91.32% for enzyme classification, which is much better than that of the BLAST and PSI-BLAST based method, also outperforms several existed works. The results indicate that protein functional domain composi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638374 Sun, 27 May 2007 03:43:46 +0100 638374 http://www.medworm.com/index.php?rid=638373&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500037%26dopt%3DAbstract Authors: Belonogova NM, Axenovich TI The likelihood approach is common in linkage analysis of large extended pedigrees. Various peeling procedures, based on the conditional independence of separate parts of a pedigree, are typically used for likelihood calculations. A peeling order may significantly affect the complexity of such calculations, particularly for pedigrees with loops or when many pedigrees members have unknown genotypes. Several algorithms have been proposed to address this problem for pedigrees with loops. However, the problem has not been solved for pedigrees without loops until now. In this paper, we suggest a new graph theoretic algorithm for optimal selection of peeling order in zero-loop pedigrees with incomplete genotypic information. It is especially useful when mu... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638373 Sun, 27 May 2007 03:43:46 +0100 638373 http://www.medworm.com/index.php?rid=638372&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500038%26dopt%3DAbstract Authors: Singhal M, Domico K The importance of understanding biological interaction networks has fueled the development of numerous interaction data generation techniques, databases and prediction tools. However, not all prediction tools and databases predict interactions with one hundred percent accuracy. Generation of high-confidence interaction networks formulates the first step towards deciphering unknown protein functions, determining protein complexes and inventing drugs. The CABIN: Collective Analysis of Biological Interaction Networks software is an exploratory data analysis tool that enables analysis and integration of interactions evidence obtained from multiple sources, thereby increasing the confidence of computational predictions as well as validating experimental observat... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638372 Sun, 27 May 2007 03:43:46 +0100 638372 http://www.medworm.com/index.php?rid=638371&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500039%26dopt%3DAbstract Authors: Taylor WR The current knowledge on topological knots in protein structure is reviewed, considering in turn, knots with three, four and five strand crossings. The latter is the most recent to be identified and has two distinct topological forms. The knot observed in the protein structure is the form that requires the least number of strand crossings to become un-knotted. The position of the chain termini must also correspond to a position that allows (un) knotting in one move. This is postulated as a general property of protein knots and other more complex knots with this property are proposed as the next most likely knots that might be found in a protein. It is also noted that the "Jelly-roll" fold found in some all-beta proteins would provide likely candidates. Alternative me... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638371 Sun, 27 May 2007 03:43:46 +0100 638371 http://www.medworm.com/index.php?rid=638370&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17500040%26dopt%3DAbstract This study was to model the 3-D structure of the zymogen, followed by intensive molecular dynamics (MD) simulations to identify the most probable 3-D model and to study the dynamic structural behavior of the zymogen for understanding the effects of pro-segment on the function of the enzyme. The results revealed that the dropping in catalytic activity of the beta-secretase zymogen could be attributed to the occupation of the entrance of the catalytic site of the zymogen by its pro-segment. On the other hand, the partial catalytic activity of the zymogen could be explained by high fluctuation of the pro-segment in comparison with that of other zymogens, resulting in the occasionally exposure of the catalytic site for access its substrate APP. Indeed, steered MD (SMD) simulation revealed a we... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=638370 Sun, 27 May 2007 03:43:46 +0100 638370 http://www.medworm.com/index.php?rid=543597&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17350341%26dopt%3DAbstract Authors: Jin WB, Wu FL, Kong D, Guo AG MicroRNAs (miRNAs) are a group of short ( approximately 22nt) noncoding RNAs that specifically regulate cellular gene expression at the post-transcriptional level. miRNA precursors (pre-miRNAs), which are imperfect stem loop structures of approximately 70nt, are processed into mature miRNAs by cellular RNases III. To date, hundreds of miRNAs and their corresponding targets have been reported in kinds of species. Although only a few of these miRNA/target pairs have been functionally verified, some do play important roles in regulating normal development and physiology. Several viruses (e.g. the Epstein-Barr virus and human herpesvirus Kaposi's sarcoma-associated herpesvirus) has been reported to encode miRNAs. Here, we extend the analysis of miRNA-... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543597 Sun, 01 Apr 2007 04:00:00 +0100 543597 http://www.medworm.com/index.php?rid=543596&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17363328%26dopt%3DAbstract Authors: Toropov AA, Leszczynska D, Leszczynski J Components of the chiral vector of carbon nanotubes have been examined in role of structural descriptors. Two-variable models of water solubility and octanol water partition coefficient calculated with components of the chiral vectors have quite good statistical characteristics. These are in case of the water solubility: n=8, r(2)=0.99998, s=0.05338, F=126,611 (training set); n=8, r(2)=0.9999, s=0.09329, F=674,556 (test set) and in case of octanol water partition coefficient: n=8, r(2)=0.9991, s=0.3664, F=2927 (training set); n=8, r(2)=0.9996, s=0.2870, F=5928 (test set). PMID: 17363328 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543596 Sun, 01 Apr 2007 04:00:00 +0100 543596 http://www.medworm.com/index.php?rid=543593&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17363329%26dopt%3DAbstract Authors: Wang Y, Feng E, Wang R Haplotype reconstruction, based on aligned single nucleotide polymorphism (SNP) fragments, is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. This paper first presents two distance functions, which are used to measure the difference degree and similarity degree between SNP fragments. Based on the two distance functions, a clustering algorithm is proposed in order to solve MEC model. The algorithm involves two sections. One is to determine the initial haplotype pair, the other concerns with inferring true haplotype pair by re-clustering. The comparison results prove that our algorithm utilizing two distance functions is effective and feasible. PMID: 17363329 [PubMed - in process] (Source:... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543593 Sun, 01 Apr 2007 04:00:00 +0100 543593 http://www.medworm.com/index.php?rid=543591&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17368104%26dopt%3DAbstract Authors: Zhang Y, Zheng N, Nan P, Cao Y, Hasegawa M, Zhong Y As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543591 Sun, 01 Apr 2007 04:00:00 +0100 543591 http://www.medworm.com/index.php?rid=543589&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17374510%26dopt%3DAbstract Authors: Zhang Y, Zheng N, Zhong Y The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational characterization and design of RBD-mediated receptor recognition and antibody neutralization. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics protocols. And the calculations predict a number of single substitutions on RBD, receptor or antibody that could remarkably elevate the binding affinities of those complexes. It is reasonable to anticipate our structure-based computati... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543589 Sun, 01 Apr 2007 04:00:00 +0100 543589 http://www.medworm.com/index.php?rid=543587&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17379577%26dopt%3DAbstract Authors: Gomathi NS, Sameer H, Kumar V, Balaji S, Dustackeer VN, Narayanan PR Che12 is a temperate Chennai phage infecting Mycobacterium tuberculosis. The nucleotide sequence of the 52,047bp linear double stranded DNA genome has a GC content of 62.9% with 70 putative ORFs identified. Functions are assigned to 24 genes based on the similarity of the predicted products to known proteins. Che12 genome is highly similar to mycobacteriophage L5 and D29 genomes. The overall genome similarity of Che12 to L5 is 82.5% and D29 is 81.5%. The genes attributing to lysogeny such as integrase, excisionase and repressor protein are identified. The attachment site of Che12 genome attP is homologous to attB sites of Mycobacterium smegmatis and M. tuberculosis. Similarities between certain phage gene pro... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543587 Sun, 01 Apr 2007 04:00:00 +0100 543587 http://www.medworm.com/index.php?rid=543585&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17387043%26dopt%3DAbstract Authors: Gharaibeh RZ, Fodor AA, Gibas CJ High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays. PMID: 17387043 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543585 Sun, 01 Apr 2007 04:00:00 +0100 543585 http://www.medworm.com/index.php?rid=543583&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17392026%26dopt%3DAbstract Authors: Yang XD, Melnik RV The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. A stochastic model is derived on the basis of the balance equation for forces acting on the chain. The Euler method is applied to the solution of the model. The extensions of DNA molecules for different Weissenberg numbers are analyzed. Comparison with the experimental results available in the literature is carried out to estimate the contribution of the effect of internal viscosity. PMID: 17392026 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543583 Sun, 01 Apr 2007 04:00:00 +0100 543583 http://www.medworm.com/index.php?rid=543581&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17392027%26dopt%3DAbstract Authors: Haeri HH, Hashemianzadeh SM, Monajjemi M Most of the previously theoretical studies about the stochastic nature of the IP3R calcium release channel gating use the chemical master equation (CME) approach. Because of the limitations of this approach we have used a stochastic simulation algorithm (SSA) presented by Gillespie. A single subunit of De Young-Keizer (DYK) model was simulated using Gillespie algorithm. The model has been considered in its complete form with eight states. We investigate the conditions which affect the open state of the model. Calcium concentrations were the subject of fluctuation in the previous works while in this study the population of the states is the subject of stochastic fluctuations. We found out that decreasing open probability is a function of... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543581 Sun, 01 Apr 2007 04:00:00 +0100 543581 http://www.medworm.com/index.php?rid=543578&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17392028%26dopt%3DAbstract Authors: Tsoi LC, Zheng WJ A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store microarray data by using array data type in an object-relational database management system-PostgreSQL. The implemented database can store all the microarray data from the same chip in an array data structure. The variable-length array data type in PostgreSQL can store mi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543578 Sun, 01 Apr 2007 04:00:00 +0100 543578 http://www.medworm.com/index.php?rid=543574&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17392029%26dopt%3DAbstract Authors: Mordvitsev DY, Polyak YL, Kuzmin DA, Levtsova OV, Tourleigh YV, Utkin YN, Shaitan KV, Tsetlin VI Weak toxins are the "three-fingered" snake venoms toxins grouped together by having an additional disulfide in the N-terminal loop I. In general, weak toxins have low toxicity, and biological targets have been identified for some of them only, recently by detecting the effects on the nicotinic acetylcholine receptors (nAChR). Here the methods of docking and molecular dynamics simulations are used for comparative modeling of the complexes between four weak toxins of known spatial structure (WTX, candoxin, bucandin, gamma-bungarotoxin) and nAChRs. WTX and candoxin are those toxins whose blocking of the neuronal alpha7- and muscle-type nAChR has been earlier shown in binding assays an... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543574 Sun, 01 Apr 2007 04:00:00 +0100 543574 http://www.medworm.com/index.php?rid=543572&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17392030%26dopt%3DAbstract Authors: Liu F, Wu B It has recently been shown that cancer genes (oncogenes) tend to have heterogeneous expressions across disease samples. So it is reasonable to assume that in a microarray data only a subset of disease samples will be activated (often referred to as outliers), which presents some new challenges for statistical analysis. In this paper, we study the multi-class cancer outlier differential gene expression detection. Statistical methods will be proposed to take into account the expression heterogeneity. Through simulation studies and application to public microarray data, we will show that the proposed methods could provide more comprehensive analysis results and improve upon the traditional differential gene expression detection methods, which often ignore the expressi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543572 Sun, 01 Apr 2007 04:00:00 +0100 543572 http://www.medworm.com/index.php?rid=543570&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17416336%26dopt%3DAbstract Authors: Hernandez-Mendoza A, Quinto C, Segovia L, Perez-Rueda E The resistance-nodulation-cell division (RND) protein family is a ubiquitous group of proteins primarily present in bacteria. These proteins, involved in the transport of multiple drugs across the cell envelope in bacteria, exhibit broad substrate specificity and act like efflux pumps. In this work, a protein belonging to the RND protein family, AcrB of Escherichia coli was used as a working model to predict in silico the compounds transported by 47 RND proteins. From AcrB we extracted and clustered 14 amino acids directly involved in substrate interactions. This clustering provides enough information to identify 16 groups that correlates with the ligand they extrude, such as proteins expelling aromatic hydrocarbons (SrpB... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543570 Sun, 01 Apr 2007 04:00:00 +0100 543570 http://www.medworm.com/index.php?rid=543565&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17416337%26dopt%3DAbstract Authors: Shah AR, Oehmen CS, Harper J, Webb-Robertson BJ A significant challenge in homology detection is to identify sequences that share a common evolutionary ancestor, despite significant primary sequence divergence. Remote homologs will often have less than 30% sequence identity, yet still retain common structural and functional properties. We demonstrate a novel method for identifying remote homologs using a support vector machine (SVM) classifier trained by fusing sequence similarity scores and subcellular location prediction. SVMs have been shown to perform well in a variety of applications where binary classification of data is the goal. At the same time, data fusion methods have been shown to be highly effective in enhancing discriminative power of data. Combining these two ap... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543565 Sun, 01 Apr 2007 04:00:00 +0100 543565 http://www.medworm.com/index.php?rid=543621&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17097351%26dopt%3DAbstract Authors: Sackmann A, Formanowicz D, Formanowicz P, Koch I, Blazewicz J In the paper a Petri net based model of the human body iron homeostasis is presented and analyzed. The body iron homeostasis is an important but not fully understood complex process. The modeling of the process presented in the paper is expressed in the language of Petri net theory. An application of this theory to the description of biological processes allows for very precise analysis of the resulting models. Here, such an analysis of the body iron homeostasis model from a mathematical point of view is given. PMID: 17097351 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543621 Thu, 01 Feb 2007 05:00:00 +0100 543621 http://www.medworm.com/index.php?rid=543609&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17218151%26dopt%3DAbstract Authors: Levine HA, Nilsen-Hamilton M Systematic evolution of ligands by exponential enrichment (SELEX) is a procedure by which a mixture of nucleic acids that vary in sequence can be separated into pure components with the goal of isolating those with specific biochemical activities. The basic idea is to combine the mixture with a specific target molecule and then separate the target-NA complex from the resulting reaction. The target-NA complex is then separated by mechanical means (for example by filtration), the NA is then eluted from the complex, amplified by polymerase chain reaction (PCR) and the process repeated. After several rounds, one should be left with a pool of [NA] that consists mostly of the species in the original pool that best binds to the target. In Irvine et al. [I... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543609 Thu, 01 Feb 2007 05:00:00 +0100 543609 http://www.medworm.com/index.php?rid=543607&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17257898%26dopt%3DAbstract Authors: Michel CJ We develop here an analytical evolution model based on a trinucleotide mutation matrix 64x64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites and with non-zero elements on its main diagonal. It generalizes the previous models based on the nucleotide mutation matrices 4x4 and the trinucleotide mutation matrices 64x64 with zero elements on its main diagonal. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. Furthermore, applications of this model allow to generalize an evolutionary analytical solution of the common circular code of eukaryotes and prokaryotes and also to derive a codon phylogenetic distance... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543607 Thu, 01 Feb 2007 05:00:00 +0100 543607 http://www.medworm.com/index.php?rid=543605&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17270497%26dopt%3DAbstract Authors: Ji X, Chen H, Xiao Y In this paper, we analyze the symmetries of beta-barrel proteins at both structure and sequence levels by using a modified recurrent quantification analysis. It shows that the structures and sequences have the same two-fold symmetry, although the later diverged considerably. This result may be helpful to understand the mechanism of protein evolution. PMID: 17270497 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543605 Thu, 01 Feb 2007 05:00:00 +0100 543605 http://www.medworm.com/index.php?rid=543603&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17270498%26dopt%3DAbstract Authors: Kazemian M, Moshiri B, Nikbakht H, Lucas C Improvement of prediction accuracy of the protein secondary structure is essential for further developments of the whole field of protein research. In this paper, the expertness of protein secondary structure prediction engines has been studied in three levels and a new criterion has been introduced in the third level. This criterion could be considered as an extension of the previous ones based on amino acid index. Using this new criterion, the expertness of some high score secondary structure prediction engines has been reanalyzed and some hidden facts have been discovered. The results of this new assessment demonstrated that a noticeable harmony has been existed among each amino acid prediction behavior in all engines. This harmony... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543603 Thu, 01 Feb 2007 05:00:00 +0100 543603 http://www.medworm.com/index.php?rid=543601&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17275412%26dopt%3DAbstract Authors: Toropov AA, Benfenati E Simplified Molecular Input Line Entry System (SMILES) nomenclature has been used as elucidating the molecular structure in construction of the quantitative structure-activity relationships (QSAR) for predicting bee toxicity. On the basis of the symbols used in the SMILES notation numerical parameters have been obtained, which are simple and fast to calculate. The method has been used to develop a QSAR model to predict toxicity of pesticides on bees. Results on a heterogeneous set of pesticides are good. Statistical characteristics of this model are: n=85, R2=0.68, s=0.82, F=180 (training set); n=20, R2=0.72, s=0.68, F=46 (test set). PMID: 17275412 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543601 Thu, 01 Feb 2007 05:00:00 +0100 543601 http://www.medworm.com/index.php?rid=543599&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17303535%26dopt%3DAbstract Authors: Su Z, Hong H, Perkins R, Shao X, Cai W, Tong W Class prediction based on DNA microarray data has been emerged as one of the most important application of bioinformatics for diagnostics/prognostics. Robust classifiers are needed that use most biologically relevant genes embedded in the data. A consensus approach that combines multiple classifiers has attributes that mitigate this difficulty compared to a single classifier. A new classification method named as consensus analysis of multiple classifiers using non-repetitive variables (CAMCUN) was proposed for the analysis of hyper-dimensional gene expression data. The CAMCUN method combined multiple classifiers, each of which was built from distinct, non-repeated genes that were selected for effectiveness in class differentiation... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543599 Thu, 01 Feb 2007 05:00:00 +0100 543599 http://www.medworm.com/index.php?rid=543626&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17000135%26dopt%3DAbstract Authors: Huang LT, Gromiha MM, Hwang SF, Ho SY Knowing the mechanisms by which protein stability change is one of the most important and valuable tasks in molecular biology. The conventional methods of predicting protein stability changes mainly focus on improving prediction accuracy. However, it is desirable to extract domain knowledge from large databases that is beneficial to accurate prediction of the protein stability change. This paper presents an interpretable prediction tree method (named iPTREE) that produces explanatory rules to explore hidden knowledge accompanied with high prediction accuracy and consequently analyzes the factors influencing the protein stability changes. To evaluate iPTREE and the knowledge upon protein stability changes, a thermodynamic dataset consisting... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543626 Fri, 01 Dec 2006 05:00:00 +0100 543626 http://www.medworm.com/index.php?rid=543623&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17092778%26dopt%3DAbstract Authors: Toropov A, Nesmerak K, Raska I, Waisser K, Palat K Optimal descriptors calculated with Simplified Molecular Input Line Entry System (SMILES) notation have been used in quantitative structure-property relationships (QSPR) modeling electrochemical half-wave potential of benzoxazine derivatives by one-variable correlations. PMID: 17092778 [PubMed - indexed for MEDLINE] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543623 Fri, 01 Dec 2006 05:00:00 +0100 543623 http://www.medworm.com/index.php?rid=543619&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17097352%26dopt%3DAbstract Authors: Valavanis IK, Bagos PG, Emiris IZ The location of the membrane lipid bilayer relative to a transmembrane protein structure is important in protein engineering. Since it is not present on the determined structures, it is essential to automatically define the membrane embedded protein region in order to test mutation effects or to design potential drugs. beta-Barrel transmembrane proteins, present in nature as outer membrane proteins (OMPs), comprise one of the two transmembrane protein fold classes. Lately, the number of their determined structures has increased and this enables the implementation and evaluation of structure-based annotation methods and their more comprehensive study. In this paper, we propose two new algorithms for (i) the geometric modelling of beta-barrels a... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543619 Fri, 01 Dec 2006 05:00:00 +0100 543619 http://www.medworm.com/index.php?rid=543617&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17098476%26dopt%3DAbstract Authors: Zhang S, Ning X, Zhang XS Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein-protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experime... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543617 Fri, 01 Dec 2006 05:00:00 +0100 543617 http://www.medworm.com/index.php?rid=543615&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17112785%26dopt%3DAbstract Authors: Kim JR, Cho KH E. coli has two-component systems composed of histidine kinase proteins and response regulator proteins. For a given extracellular stimulus, a histidine kinase senses the stimulus, autophosphorylates and then passes the phosphates to the cognate response regulators. The histidine kinase in an orthodox two-component system has only one histidine domain where the autophosphorylation occurs, but a histidine kinase in some unusual two-component systems (unorthodox two-component systems) has two histidine domains and one aspartate domain. So, the unorthodox two-component systems have more complex phosphorelay mechanisms than orthodox two-component systems. In general, the two-component systems are required to promptly respond to external stimuli for survival of E. co... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543615 Fri, 01 Dec 2006 05:00:00 +0100 543615 http://www.medworm.com/index.php?rid=543613&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17123865%26dopt%3DAbstract Authors: Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA MicroRNAs (miRNAs) are one class of newly identified riboregulators of gene expression in many eukaryotic organisms. They play important roles in multiple biological and metabolic processes, including developmental timing, signal transduction, cell maintenance and differentiation, diseases and cancers. miRNAs regulate gene expression at the posttranscriptional level by directly cleaving targeted mRNAs or repressing translation. Although the founding members of miRNAs were discovered by genetic screening approaches, experimental approaches were limited by their low efficiency, time consuming, and high cost. As an alternative, computational approaches were developed. Computational approaches for identifying miRNAs are based on the fol... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543613 Fri, 01 Dec 2006 05:00:00 +0100 543613 http://www.medworm.com/index.php?rid=543611&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17126079%26dopt%3DAbstract We present a new method, link-test, to select prostate cancer biomarkers from SELDI mass spectrometry and microarray data sets. Biomarkers selected by link-test are supported by data sets from both mRNA and protein levels, and therefore results in improved robustness. Link-test determines the level of significance of the association between a microarray marker and a specific mass spectrum marker by constructing background mass spectra distributions estimated by all human protein sequences in the SWISS-PROT database. The data set consist of both microarray and mass spectrometry data from prostate cancer patients and healthy controls. A list of statistically justified prostate cancer biomarkers is reported by link-test. Cross-validation results show high prediction accuracy using the identif... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543611 Fri, 01 Dec 2006 05:00:00 +0100 543611 http://www.medworm.com/index.php?rid=543652&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16872904%26dopt%3DAbstract Authors: Axenovich TI, Aulchenko YS Finding genes for complex traits is one of the major challenges of modern human genetics. Current developments of molecular techniques facilitated use of large pedigrees and marker sets of thousands of single-nucleotide polymorphisms (SNPs). However, one of the problems occurring in statistical analysis of such large data sets is that the likelihood is very low and underflow may easily occur. In this work we describe a method permitting to avoid underflow during computation of a likelihood function, using different algorithms. Our method makes practically possible analysis of thousands of individuals and thousands of SNPs. The method is easy to implement without major change of the code of existing programs. It also helps to reduce the amount of comp... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543652 Sun, 01 Oct 2006 04:00:00 +0100 543652 http://www.medworm.com/index.php?rid=543650&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16872905%26dopt%3DAbstract Authors: Kedarisetti KD, Kurgan L, Dick S Protein structural class describes the overall folding type of a protein or its domain. A number of methods were developed to predict protein structural class based on its primary sequence. The homology of the predicted sequences with respect to the training sequences is a key attribute for the prediction performance. In this article we investigated the FDOD method developed by Jin et al. [Jin, L., Fang, W., Tang, H., 2003. Prediction of protein structural classes by a new measure of information discrepancy. Comput. Biol. Chem. 27, 373-380], which gave high prediction accuracy on a low homology dataset, and we empirically confirmed that the reported results were an artifact of improper implementation. PMID: 16872905 [PubMed - in process] (S... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543650 Sun, 01 Oct 2006 04:00:00 +0100 543650 http://www.medworm.com/index.php?rid=543644&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16945587%26dopt%3DAbstract Authors: Blazewicz J, Glover F, Kasprzak M, Markiewicz WT, Oğuz C, Rebholz-Schuhmann D, Swiercz A DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic algorithm for isothermic and standard sequencing that incorporates the concept of structured combinations. The algorithm is then compared with other methods designed for handling errors that arise in standard and isothermic SBH approaches. DNA sequences used for testing are taken from GenBank. The set of instances for testing was divide... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543644 Sun, 01 Oct 2006 04:00:00 +0100 543644 http://www.medworm.com/index.php?rid=543642&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16963318%26dopt%3DAbstract Authors: Zhang T, Ding Y, Chou KC The function of eukaryotic protein is closely correlated with its subcellular location. The number of newly found protein sequences entering into data banks is rapidly increasing with the success of human genome project. It is highly desirable to predict a protein subcellular automatically from its amino acid sequence. In this paper, amino acid hydrophobic patterns and average power-spectral density (APSD) are introduced to define pseudo amino acid composition. The covariant-discriminant predictor is used to predict subcellular location. Immune-genetic algorithm (IGA) is used to find the fittest weight factors which are very important in this method. As such, high success rates are obtained by both self-consistency test (86%) and jackknife test (73%). ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543642 Sun, 01 Oct 2006 04:00:00 +0100 543642 http://www.medworm.com/index.php?rid=543640&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16971184%26dopt%3DAbstract Authors: Stepanova M, Lin F, Lin VC Identification of hormone response elements (HREs) is essential for understanding the mechanism of hormone-regulated gene expression. To date, there has been a lack of effective bioinformatics tools for recognition of specific HRE such as Progesterone Response Elements (PRE). In this paper, a comprehensive survey and comparison of in silico methods is conducted for establishing a more accurate statistic model. Homogeneity of steroid HRE is analyzed and a reliable training dataset is constructed through extensive searching for experimentally validated response elements from more than 150 literature sources. Based on the observation that the verified HREs carry di-nucleotide preservation in comparison with uniform nucleotide distributions, both mono an... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543640 Sun, 01 Oct 2006 04:00:00 +0100 543640 http://www.medworm.com/index.php?rid=543638&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16978924%26dopt%3DAbstract Authors: Li MH, Wang XL, Lin L, Liu T Protein-protein interactions (PPIs) prediction is an important issue in biology. Recently many computational methods have been proposed to determine PPIs. However, there is no golden standard dataset for these methods now. Furthermore, there exists different quality among training examples and the quality is always ignored by the current methods. In the condition of low-quality examples, the system should tolerate the data noise. Example weighting strategy is used in this paper to build a robust system and solve the problem of data noise. Training examples are investigated and a new example selecting/using strategy is proposed. Training example weighting method based on confidence is proposed. Different weight setting strategies are discussed and t... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543638 Sun, 01 Oct 2006 04:00:00 +0100 543638 http://www.medworm.com/index.php?rid=543636&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16979381%26dopt%3DAbstract Authors: Lai Y It has been shown that the generalized F-statistics can give satisfactory performances in identifying differentially expressed genes with microarray data. However, for some complex diseases, it is still possible to identify a high proportion of false positives because of the modest differential expressions of disease related genes and the systematic noises of microarrays. The main purpose of this study is to develop statistical methods for Affymetrix microarray gene expression data so that the impact on false positives from non-expressed genes can be reduced. I proposed two novel generalized F-statistics for identifying differentially expressed genes and a novel approach for estimating adjusting factors. The proposed statistical methods systematically combine filtering o... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543636 Sun, 01 Oct 2006 04:00:00 +0100 543636 http://www.medworm.com/index.php?rid=543634&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16982212%26dopt%3DAbstract Authors: Jonassen I, Klose D, Taylor WR A method is described for the refinement of rough protein models based on finding a selection of structural fragments that match the model. Unlike most fragment-based methods, these are not necessarily contiguous in the sequence and form a tiling (tessellation) that covers most of the structure. The residue positions of the fragments are then used as a target for the model atoms to generate a revised model which is used as the basis of a subsequent pattern definition and search. The method was shown to improve the recognition of the native fold in a series of decoys largely as a result of improved secondary structure representation. PMID: 16982212 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543634 Sun, 01 Oct 2006 04:00:00 +0100 543634 http://www.medworm.com/index.php?rid=543632&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16987707%26dopt%3DAbstract Authors: Durmuş Tekir S, Cakir T, Ulgen KO The human red blood cell (RBC) metabolism is investigated by calculating steady state fluxes using constraint-based stoichiometric modeling approaches. For the normal RBC metabolism, flux balance analysis (FBA) is performed via optimization of various alternative objective functions, and the maximization of production of ATP and NADPH is found to be the primary objective of the RBC metabolism. FBA and two novel approaches, minimization of metabolic adjustment (MOMA) and regulatory on-off minimization (ROOM), which can describe the behavior of the metabolic networks in case of enzymopathies, are applied to observe the relative changes in the flux distribution of the deficient network. The deficiencies in several enzymes in RBC metabolism are i... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543632 Sun, 01 Oct 2006 04:00:00 +0100 543632 http://www.medworm.com/index.php?rid=543630&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16987708%26dopt%3DAbstract Authors: Chen CF, Feng X, Szeto J Gene expression profiling by microarray technology is usually difficult to interpret into a simpler pattern. One approach to resolve the complexity of gene expression profiles is the application of artificial neural networks (ANNs). A potential difficulty in this strategy, however, is that the non-linear nature of ANN makes it essentially a 'black-box' computation process. Addition of a fuzzy logic approach is useful because it can complement ANN by explicitly specifying membership function during computation. We employed a hybrid approach of neural network and fuzzy logic to further analyze a published microarray study of gene responses to eight bacteria in human macrophages. The original analysis by hierarchical clustering found common gene responses... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543630 Sun, 01 Oct 2006 04:00:00 +0100 543630 http://www.medworm.com/index.php?rid=543628&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16996313%26dopt%3DAbstract Authors: Galat A The powerful immunosuppressive drugs such as FK506 and its derivatives induce some regeneration and protection of neurons from ischaemic brain injury and some other neurological disorders. The drugs form complexes with diverse FKBPs but apparently the FKBP52/FK506 complex was shown to be involved in the protection and regeneration of neurons. We used several different sequence attributes in searching diverse genomic databases for similar motifs as those present in the FKBPs. A Fortran library of algorithms (Par_Seq) has been designed and used in searching for the similarity of sequence motifs extracted from the multiple sequence alignments of diverse groups of proteins (query motifs) and the target motifs which are encoded in various genomes. The following sequence att... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543628 Sun, 01 Oct 2006 04:00:00 +0100 543628 http://www.medworm.com/index.php?rid=543664&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16797236%26dopt%3DAbstract Authors: Deng R, Huang M, Wang J, Huang Y, Yang J, Feng J, Wang X Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method. PMID: 16797236 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543664 Tue, 01 Aug 2006 04:00:00 +0100 543664 http://www.medworm.com/index.php?rid=543662&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16798093%26dopt%3DAbstract Authors: Gorodkin J, Havgaard JH, Ensterö M, Sawera M, Jensen P, Ohman M, Fredholm M The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature miRNAs in their genomic contexts. We have compared profiles of mature miRNAs within their genomic context of the 5' and 3' stemloop precursor arms and we find asymmetry between mature sequences of the 5' and 3' stemloop precursor arms. The main observation is that vertebrate organisms have a characteristic motif on the 5' arm which is in contrast to the 3' arm motif which mainly show the conserved U at the position of the mature... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543662 Tue, 01 Aug 2006 04:00:00 +0100 543662 http://www.medworm.com/index.php?rid=543660&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16798094%26dopt%3DAbstract Authors: Brylinski M, Konieczny L, Roterman I A model of hydrophobic collapse, which is treated as the driving force for protein folding, is presented. This model is the superposition of three models commonly used in protein structure prediction: (1) 'oil-drop' model introduced by Kauzmann, (2) a lattice model introduced to decrease the number of degrees of freedom for structural changes and (3) a model of the formation of hydrophobic core as a key feature in driving the folding of proteins. These three models together helped to develop the idea of a fuzzy-oil-drop as a model for an external force field of hydrophobic character mimicking the hydrophobicity-differentiated environment for hydrophobic collapse. All amino acids in the polypeptide interact pair-wise during the folding proce... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543660 Tue, 01 Aug 2006 04:00:00 +0100 543660 http://www.medworm.com/index.php?rid=543658&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16798095%26dopt%3DAbstract In this report, we have analyzed the conformational changes of p47phox-p22phox complexes of wild-type and three mutants, which have been detected in CGD patients, using molecular dynamics simulations. We have found that in the wild-type, two basal planes of PPII prism in cytoplasmic region of p22phox interacted with N-SH3 and C-SH3. In contrast, in the modeled mutants, the residue at the ape of PPII helix, which interacts simultaneously with both of the tandem SH3 domains in the wild-type, moved toward C-SH3. Furthermore, interaction energies of the cytoplasmic region of p22phox with C-SH3 tend to decrease in these mutants. All these findings led us to conclude that interactions between N-SH3 of p47phox and PPII helix, which is formed by cytoplasmic region of p22phox, may play a significan... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543658 Tue, 01 Aug 2006 04:00:00 +0100 543658 http://www.medworm.com/index.php?rid=543656&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16798096%26dopt%3DAbstract Authors: Roy S, Schnell S, Radivojac P Vertebrate segmentation has been proved to be under a strict temporal control governed by a biological clock, known as the segmentation clock. The present experimental evidence suggests that the segmentation clock initiates and maintains its periodic cycle by the periodic activation or inhibition of the Notch signaling pathway as well as the periodic autoregulation of the cyclic genes themselves. In this paper, we investigate the structural and evolutionary properties of the Notch pathway proteins involved in the mice segmentation clock and computationally identify the interaction map within the Notch signaling pathway. The results of our analysis strongly indicate that most of the pathway proteins are intrinsically disordered and that the mechani... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543656 Tue, 01 Aug 2006 04:00:00 +0100 543656 http://www.medworm.com/index.php?rid=543654&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16861039%26dopt%3DAbstract Authors: Dubey A, Realff MJ, Lee JH, Bommarius AS It is known that in the three-dimensional structure of a protein, certain amino acids can interact with each other in order to provide structural integrity or aid in its catalytic function. If these positions are mutated the loss of this interaction usually leads to a non-functional protein. Directed evolution experiments, which probe the sequence space of a protein through mutations in search for an improved variant, frequently result in such inactive sequences. In this work, we address the use of machine learning algorithms, Boolean learning and support vector machines (SVMs), to find such pairs of amino acid positions. The recombination method of imparting mutations was simulated to create in silico sequences that were used as traini... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543654 Tue, 01 Aug 2006 04:00:00 +0100 543654 http://www.medworm.com/index.php?rid=543648&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16880117%26dopt%3DAbstract Authors: Manninen T, Linne ML, Ruohonen K Mathematical modeling and simulation of dynamic biochemical systems are receiving considerable attention due to the increasing availability of experimental knowledge of complex intracellular functions. In addition to deterministic approaches, several stochastic approaches have been developed for simulating the time-series behavior of biochemical systems. The problem with stochastic approaches, however, is the larger computational time compared to deterministic approaches. It is therefore necessary to study alternative ways to incorporate stochasticity and to seek approaches that reduce the computational time needed for simulations, yet preserve the characteristic behavior of the system in question. In this work, we develop a computational frame... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543648 Tue, 01 Aug 2006 04:00:00 +0100 543648 http://www.medworm.com/index.php?rid=543646&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16880118%26dopt%3DAbstract Authors: Oğul H, Mumcuoğlu EU A new method based on probabilistic suffix trees (PSTs) is defined for pairwise comparison of distantly related protein sequences. The new definition is adopted in a discriminative framework for protein classification using pairwise sequence similarity scores in feature encoding. The framework uses support vector machines (SVMs) to separate structurally similar and dissimilar examples. The new discriminative system, which we call as SVM-PST, has been tested for SCOP family classification task, and compared with existing discriminative methods SVM-BLAST and SVM-Pairwise, which use BLAST similarity scores and dynamic-programming-based alignment scores, respectively. Results have shown that SVM-PST is more accurate than SVM-BLAST and competitive with SVM-Pa... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543646 Tue, 01 Aug 2006 04:00:00 +0100 543646 http://www.medworm.com/index.php?rid=543681&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16600687%26dopt%3DAbstract Authors: Takasaki S, Kawamura Y, Konagaya A Short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells but varies markedly in its gene-silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported recently, there are only a few consistencies among them. This makes it difficult to select effective siRNA sequences in mammalian genes. Here, we propose a new method for selecting effective siRNA target sequences on the basis of the self-organizing map (SOM) technique and statistical significance analyses for a large number of effective siRNAs. In the proposed method, the score is defined as a gene degradation measure. The effectiveness for the proposed method was confirmed by evaluating effe... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543681 Thu, 01 Jun 2006 04:00:00 +0100 543681 http://www.medworm.com/index.php?rid=543679&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16650806%26dopt%3DAbstract In this study, I propose a likelihood-based method coupled with an expectation-maximization (E-M) algorithm for estimating the proportion of differentially expressed genes. The proposed method has favorable performances if either (i) the P values of differentially expressed genes are homogeneously distributed or (ii) the proportion of differentially expressed genes is relatively small. In both of these situations, I showed through simulations that the proposed method gave satisfactory performances when it was compared to other existing methods. As applications, these methods were applied to two microarray gene expression data sets generated from different platforms. PMID: 16650806 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543679 Thu, 01 Jun 2006 04:00:00 +0100 543679 http://www.medworm.com/index.php?rid=543677&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16651027%26dopt%3DAbstract Authors: Srividhya J, Schnell S A number of enzyme digestion assays show apparent first-order kinetics of reactant depletion. There are four possible explanations of this phenomenon: (i) the reaction is dominated by a first-order limiting step, (ii) the digestion follows a pseudo-first-order kinetics under the excess of a reactant species, (iii) the first-order kinetics is only applicable to the slow transient of the reaction, or (iv) the aggregate behavior of the reaction pathway produces behavior indistinguishable from the first-order kinetics. In this paper, we investigate the kinetics for protein digestion by formulating rate equations for two proposed mechanisms, namely the one-by-one mechanism and the zipper mechanism. Our analysis shows that the kinetics of protein digestion fol... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543677 Thu, 01 Jun 2006 04:00:00 +0100 543677 http://www.medworm.com/index.php?rid=543675&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16675303%26dopt%3DAbstract Authors: Eargle J, Luthey-Schulten Z An important part of protein structure characterization is the determination of excluded space such as fissures in contact interfaces, pores, inaccessible cavities, and catalytic pockets. We introduce a general tessellation method for visualizing the dual space around, within, and between biological molecules. Using Delaunay triangulation, a three-dimensional graph is constructed to provide a displayable discretization of the continuous volume. This graph structure is also used to compare the dual space of a system in two different states. Tessellator, a cross-platform implementation of the algorithm, is used to analyze the cavities within myoglobin, the protein-RNA docking interface between aspartyl-tRNA synthetase and tRNA(Asp), and the ammonia ch... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543675 Thu, 01 Jun 2006 04:00:00 +0100 543675 http://www.medworm.com/index.php?rid=543673&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16678490%26dopt%3DAbstract Authors: Marchut AJ, Hall CK Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglutamine chains 16 residues long at a concentration of 5 mM spontaneously formed large beta sheets which curved to form tube-like annular structures that resemble beta barrels. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms depending on the residue being modeled. Our resul... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543673 Thu, 01 Jun 2006 04:00:00 +0100 543673 http://www.medworm.com/index.php?rid=543671&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16679066%26dopt%3DAbstract This study integrates the two metabolic pathways with the genetic regulatory circuit using the GEPASI 3.30 simulation environment, and investigates the model behavior under various nutrient conditions. Our system is successful in achieving transcriptional upregulation of the galactose metabolizing enzymes as required. Under high glucose and high galactose concentrations, the in silico yeast chooses to metabolize glucose first, after which it resorts to using the galactose available. We also show what the preferred storage macromolecules are in different metabolic pathways. PMID: 16679066 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543671 Thu, 01 Jun 2006 04:00:00 +0100 543671 http://www.medworm.com/index.php?rid=543670&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16716751%26dopt%3DAbstract Authors: Zhang GQ, Cao ZW, Luo QM, Cai YD, Li YX The operon is a specific functional organization of genes found in bacterial genomes. Most genes within operons share common features. The support vector machine (SVM) approach is here used to predict operons at the genomic level. Four features were chosen as SVM input vectors: the intergenic distances, the number of common pathways, the number of conserved gene pairs and the mutual information of phylogenetic profiles. The analysis reveals that these common properties are indeed characteristic of the genes within operons and are different from that of non-operonic genes. Jackknife testing indicates that these input feature vectors, employed with RBF kernel SVM, achieve high accuracy. To validate the method, Escherichia coli K12 and Baci... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543670 Thu, 01 Jun 2006 04:00:00 +0100 543670 http://www.medworm.com/index.php?rid=543668&cid=s_35423_79_f&fid=35423&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16720104%26dopt%3DAbstract Authors: Bagchi A, Ghosh TC Microbial redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle. These reactions are mediated by phylogenetically diverse prokaryotes containing the sulfur oxidizing gene cluster (sox). The sox gene cluster of alpha-Proteobacteria comprises of at least 15 genes, which form two transcriptional units. Recently two new orfs, which code for proteins named, SigE and ORF1, were identified in Starkeya novella. Sequence analyses reveal that SigE protein has the signature sequence of ECF-type sigma factors and a helix-turn-helix (HTH) DNA binding motif whereas ORF1 is possibly an anti ECF-sigma factor, which also has the signature sequence of the dsr family of sulfate ion binding proteins. We... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=543668 Thu, 01 Jun 2006 04:00:00 +0100 543668