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. Thu, 09 Feb 2012 22:12:27 +0100 http://www.medworm.com/index.php?rid=5657825&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%3D22301201%26dopt%3DAbstract In this study we investigated identity patterns between the last 15 nucleotides of the exonic sequence preceding the 5' splice site and the intronic sequence preceding the 3' splice site in a set of human protein-coding genes that do not exhibit intron retention. We found that almost 60% of consecutive exons and introns in human protein-coding genes share at least two identical nucleotides at their 3' ends and, on average, the sequence identity length is 2.47 nucleotides. Based on our findings we conclude that the 3' ends of exons and introns tend to have longer identical sequences within a gene than when being taken from different genes. Our results hold even if the pairs are non-consecutive in the transcription order. PMID: 22301201 [PubMed - as supplied by publisher] (Source: Comput... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5657825 Thu, 12 Jan 2012 05:00:00 +0100 5657825 http://www.medworm.com/index.php?rid=5657826&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%3D22286086%26dopt%3DAbstract Authors: Zhang Y, Zhang D, Mi G, Ma D, Li G, Guo Y, Li M, Zhu M Abstract In proteins, the number of interacting pairs is usually much smaller than the number of non-interacting ones. So the imbalanced data problem will arise in the field of protein-protein interactions (PPIs) prediction. In this article, we introduce two ensemble methods to solve the imbalanced data problem. These ensemble methods combine the based-cluster under-sampling technique and the fusion classifiers. And then we evaluate the ensemble methods using a dataset from Database of Interacting Proteins (DIP) with 10-fold cross validation. All the prediction models achieve area under the receiver operating characteristic curve (AUC) value about 95%. Our results show that the ensemble classifiers are quite effective ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5657826 Tue, 03 Jan 2012 05:00:00 +0100 5657826 http://www.medworm.com/index.php?rid=5657827&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%3D22286085%26dopt%3DAbstract Authors: Tabataba FS, Mousavi SR Abstract The Longest Common Subsequence Problem is the problem of finding a longest string that is a subsequence of every member of a given set of strings. It has applications in FPGA circuit minimization, data compression, and bioinformatics, among others. The problem is NP-hard in its general form, which implies that no exact polynomial-time algorithm currently exists for the problem. Consequently, inexact algorithms have been proposed to obtain good, but not necessarily optimal, solutions in an affordable time. In this paper, a hyper-heuristic algorithm incorporated within a constructive beam search is proposed for the problem. The proposed hyper-heuristic is based on two basic heuristic functions, one of which is new in this paper, and determine... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5657827 Fri, 30 Dec 2011 05:00:00 +0100 5657827 http://www.medworm.com/index.php?rid=5620014&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%3D22261151%26dopt%3DAbstract In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series co... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5620014 Fri, 30 Dec 2011 05:00:00 +0100 5620014 http://www.medworm.com/index.php?rid=5438882&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%3D22099628%26dopt%3DAbstract In conclusion, these results represent the first identification of virtual STATREs in the hIR gene promoter. These STATREs appear to be specifically located in the surroundings of the two EREs overlapped by various AP-1 sites. These complexes could mediate crosstalk among STATs, estrogen receptor β (ERβ), and AP-1 regulating the ERβ-mediated transcriptional repression of the hIR gene and insulin resistance in U-937 cells. PMID: 22099628 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438882 Thu, 24 Nov 2011 01:31:10 +0100 5438882 http://www.medworm.com/index.php?rid=5438881&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%3D22099629%26dopt%3DAbstract Authors: Liu Z, Li X, Zhao P, Gui J, Zheng W, Zhang Y Abstract Mitochondria are eukaryotic organelles originated from a single bacterial endosymbiosis about 2 billion years ago. One of the earliest events in the evolution of mitochondria was the acquisition of a mechanism that facilitated the import of proteins from cytosol. The mitochondrial protein import machinery consists of dozens of subunits, and they are of modular design. However, to date, it is not clear when certain component was added to the machinery. Using extensive homology searches, the evolutionary history of the mitochondrial protein import machinery was reconstructed. The results indicated that 6 of the 35 subunits have homologs in prokaryote, suggesting that they were prokaryotic origin; the major subunit gains w... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438881 Thu, 24 Nov 2011 01:31:01 +0100 5438881 http://www.medworm.com/index.php?rid=5438880&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%3D22099630%26dopt%3DAbstract Authors: Tenorio-Salgado S, Huerta-Saquero A, Perez-Rueda E Abstract Archaea represent an important and vast domain of life. This cellular domain includes a large diversity of organisms characterized as prokaryotes with basal transcriptional machinery similar to eukarya. In this work we explore the most recent findings concerning the transcriptional regulatory organization in archaeal genomes since the perspective of the DNA-binding transcription factors (TFs), such as the high proportion of archaeal TFs homologous to bacteria, the apparent deficit of TFs, only comparable to the proportion of TFs in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. We discuss an appealing hypothesis to explain the apparent deficit of TFs in archaea, bas... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438880 Thu, 24 Nov 2011 01:30:52 +0100 5438880 http://www.medworm.com/index.php?rid=5438879&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%3D22099631%26dopt%3DAbstract Authors: Mozrzymas A Abstract The extensions of generalized (molecular) graph-theoretical matrix and vector-matrix-vector procedure are considered. The elements of the generalized matrix are redefined in order to describe molecules containing heteroatoms and multiple bonds. The adjacency, distance, detour and reciprocal distance matrices of heterosystems, and corresponding vectors are derived from newly defined generalized graph matrix. The topological indices, which are most widely used in predicting physicochemical and biological properties/activities of various compounds, can be calculated from the new generalized vector-matrix-vector invariant. PMID: 22099631 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438879 Thu, 24 Nov 2011 01:30:42 +0100 5438879 http://www.medworm.com/index.php?rid=5438878&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%3D22099632%26dopt%3DAbstract In conclusion, our new method can efficiently integrate diverse data sources, and will promote the further research in drug discovery. PMID: 22099632 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438878 Thu, 24 Nov 2011 01:30:32 +0100 5438878 http://www.medworm.com/index.php?rid=5438877&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%3D22099633%26dopt%3DAbstract Authors: Omelina ES, Baricheva EM, Oshchepkov DY, Merkulova TI Abstract The transcription factor GAGA, encoded by the gene Trl, controls expression of many Drosophila melanogaster genes. We have compiled the presently largest sample (120 sites) of published nucleotide sequences with experimentally confirmed binding to GAGA protein. Analysis of the sample has demonstrated that despite an apparent structural diversity of the GAGA sites, they fall into four distinct groups, namely, (1) the sites containing two GAG trinucleotides with no more than one nucleotide substitution in each and separated by spacers with a length of 1 or 3 nucleotides (GAGnGAG and GAGnnnGAG); (2) the sites containing a single GAGAG motif; (3) (GA)(3-9) microsatellite repeats; and (4) the sites corresponding to ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438877 Thu, 24 Nov 2011 01:30:22 +0100 5438877 http://www.medworm.com/index.php?rid=5438876&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%3D22099634%26dopt%3DAbstract Authors: Tagore S, De RK Abstract BACKGROUND: A complex network of biochemical reactions present in an organism generates various biological moieties necessary for its survival. It is seen that biological systems are robust to genetic and environmental changes at all levels of organization. Functions of various organisms are sustained against mutational changes by using alternative pathways. It is also seen that if any one of the paths for production of the same metabolite is hampered, an alternate path tries to overcome this defect and helps in combating the damage. METHODOLOGY: Certain physical, chemical or genetic change in any of the precursor substrate of a biochemical reaction may damage the production of the ultimate product. We employ a quantitative approach for simulat... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5438876 Thu, 24 Nov 2011 01:30:13 +0100 5438876 http://www.medworm.com/index.php?rid=5379079&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%3D22000797%26dopt%3DAbstract In this study using computational analysis of sequenced rice genome, we identified eight and seven potential non-redundant members involved in AsA and tocochromanol biosynthetic pathways, respectively. The results reveal that the common feature of these gene promoters is the combination of light-responsive, hormone-responsive, and stress-responsive elements. These findings, together with expression analysis in the MPSS database, indicate that AsA and tocochromanols might be co-related with the complex signaling pathways involved in plant responses. PMID: 22000797 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379079 Wed, 12 Oct 2011 04:00:00 +0100 5379079 http://www.medworm.com/index.php?rid=5379078&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%3D22000798%26dopt%3DAbstract Authors: Mourão M, Schnell S, Shaw SL Abstract Microtubule polymers typically function through their collective organization into a patterned array. The formation of the pattern, whether it is a relatively simple astral array or a highly complex mitotic spindle, relies on controlled microtubule nucleation and the basal dynamics parameters governing polymer growth and shortening. We have investigated the interaction between the microtubule nucleation and dynamics parameters, using macroscopic Monte Carlo simulations, to determine how these parameters contribute to the underlying microtubule array morphology (i.e. polymer density and length distribution). In addition to the well-characterized steady state achieved between free tubulin subunits and microtubule polymer, we propose tha... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379078 Wed, 12 Oct 2011 04:00:00 +0100 5379078 http://www.medworm.com/index.php?rid=5379077&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%3D22000799%26dopt%3DAbstract This study deals with the β-catenin dependent branch of Wnt signaling and the Hedgehog signaling pathways which offer potential targeting points for cancer drug development. The identification of all proteins functioning in these signaling networks is crucial for the efforts of preventing tumor formation. Here, through integration of protein-protein interaction data and Gene Ontology annotations, Wnt/β-catenin and Hedgehog signaling networks consisting of proteins that have statistically high probability of being biologically related to these signaling pathways were reconstructed in Drosophila melanogaster. Next, by the structural network analyses, the crucial components functioning in these pathways were identified. The proteins Arm, Frizzled receptors (Fz and Fz2), Arr, Apc, Axn, Ci an... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379077 Wed, 12 Oct 2011 04:00:00 +0100 5379077 http://www.medworm.com/index.php?rid=5379076&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%3D22000800%26dopt%3DAbstract Authors: Gu J, Zhang H, Chen L, Xu S, Yuan G, Xu X Abstract Many Traditional Chinese Medicines (TCMs) are effective to relieve complicated diseases such as type II diabetes mellitus (T2DM). In this work, molecular docking and network analysis were employed to elucidate the action mechanism of a medical composition which had clinical efficacy for T2DM. We found that multiple active compounds contained in this medical composition would target multiple proteins related to T2DM and the biological network would be shifted. We predicted the key players in the medical composition and some of them have been reported in literature. Meanwhile, several compounds such as Rheidin A, Rheidin C, Sennoside C, procyanidin C1 and Dihydrobaicalin were notable although no one have reported their pharm... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379076 Wed, 12 Oct 2011 04:00:00 +0100 5379076 http://www.medworm.com/index.php?rid=5379075&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%3D22000801%26dopt%3DAbstract Authors: Yu L, Gao L, Li K, Zhao Y, Chiu DK Abstract Since cellular functionality is typically envisioned as having a hierarchical structure, we propose a framework to identify modules (or clusters) within protein-protein interaction (PPI) networks in this paper. Based on the within-module and between-module edges of subgraphs and degree distribution, we present a formal module definition in PPI networks. Using the new module definition, an effective quantitative measure is introduced for the evaluation of the partition of PPI networks. Because of the hierarchical nature of functional modules, a hierarchical agglomerative clustering algorithm is developed based on the new measure in order to solve the problem of complexes detection within PPI networks. We use gold standard sets of ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379075 Wed, 12 Oct 2011 04:00:00 +0100 5379075 http://www.medworm.com/index.php?rid=5379074&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%3D22000802%26dopt%3DAbstract Authors: Wang C, Yan RX, Wang XF, Si JN, Zhang Z Abstract Profile-profile alignment algorithms have proven powerful for recognizing remote homologs and generating alignments by effectively integrating sequence evolutionary information into scoring functions. In comparison to scoring function, the development of gap penalty functions has rarely been addressed in profile-profile alignment algorithms. Although indel frequency profiles have been used to construct profile-based variable gap penalties in some profile-profile alignment algorithms, there is still no fair comparison between variable gap penalties and traditional linear gap penalties to quantify the improvement of alignment accuracy. We compared two linear gap penalty functions, the traditional affine gap penalty (AGP) and t... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379074 Wed, 12 Oct 2011 04:00:00 +0100 5379074 http://www.medworm.com/index.php?rid=5379073&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%3D22000803%26dopt%3DAbstract Authors: Zhang Y, Zhang H, Zhou T, Zhong Y, Jin Q Abstract We employed an evolutionary genomics approach to detect genes under lineage-specific positive selection for the two closely related Mycobacterium tuberculosis strains, the virulent H37Rv and the avirulent H37Ra, with the clinical isolate CDC1551 as the outgroup. We found six H37Rv-specific and six H37Ra-specific positively selected genes, among which the former comprised a flavoprotein, a RNA polymerase sigma factor SigM, two PPE family proteins, as well as two hypothetical proteins, while the latter consisted of a dehydrogenase, a (3R)-hydroxyacyl-ACP dehydratase subunit HadA, a PPE family protein, and three PE-PGRS family proteins. Obviously, the PE/PPE/PE-PGRS family proteins were the main targets of positive selection. ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379073 Wed, 12 Oct 2011 04:00:00 +0100 5379073 http://www.medworm.com/index.php?rid=5379072&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%3D22000804%26dopt%3DAbstract Authors: Sadowski MI, Maksimiak K, Taylor WR Abstract The extraction of correlated mutations through the method of direct information (DI) provides predicted contact residue pairs that can be used to constrain the three dimensional structures of proteins. We apply this method to a large set of decoy protein folds consisting of many thousand well-constructed models, only tens of which have the correct fold. We find that DI is able to greatly improve the ranking of the true (native) fold but others still remain high scoring that would be difficult to discard due to small shifts in the core beta sheets. PMID: 22000804 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5379072 Wed, 12 Oct 2011 04:00:00 +0100 5379072 http://www.medworm.com/index.php?rid=5296124&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%3D21970031%26dopt%3DAbstract Authors: Crabbe MJ, Konopka AK PMID: 21970031 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5296124 Wed, 10 Aug 2011 04:00:00 +0100 5296124 http://www.medworm.com/index.php?rid=5174732&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%3D21864790%26dopt%3DAbstract In this study, we applied self-organizing maps (SOMs) on those complex gene expression data from different pluripotent cells, including partially reprogrammed and fully reprogrammed induced pluripotent cells (iPSCs), embryonic stem cells (ESCs), and adult stem cells came from different tissues. We showed that our SOMs have good correlation with the previously reported PluriNet of stem cells and they are pictorial diagrams which can reflect the intrinsic status of cells. PMID: 21864790 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5174732 Tue, 09 Aug 2011 23:00:00 +0100 5174732 http://www.medworm.com/index.php?rid=5174731&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%3D21864791%26dopt%3DAbstract Authors: Khan A, Majid A, Hayat M Abstract Precise information about protein locations in a cell facilitates in the understanding of the function of a protein and its interaction in the cellular environment. This information further helps in the study of the specific metabolic pathways and other biological processes. We propose an ensemble approach called "CE-PLoc" for predicting subcellular locations based on fusion of individual classifiers. The proposed approach utilizes features obtained from both dipeptide composition (DC) and amphiphilic pseudo amino acid composition (PseAAC) based feature extraction strategies. Different feature spaces are obtained by varying the dimensionality using PseAAC for a selected base learner. The performance of the individual learning mechanisms su... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5174731 Tue, 09 Aug 2011 23:00:00 +0100 5174731 http://www.medworm.com/index.php?rid=5174730&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%3D21864792%26dopt%3DAbstract Authors: Kondov I, Verma A, Wenzel W Abstract The presence of disulfide bonds in proteins has very important implications on the three-dimensional structure and folding of proteins. An adequate treatment of disulfide bonds in de-novo protein simulations is therefore very important. Here we present a computational study of a set of small disulfide-bridged proteins using an all-atom stochastic search approach and including various constraining potentials to describe the disulfide bonds. The proposed potentials can easily be implemented in any code based on all-atom force fields and employed in simulations to achieve an improved prediction of protein structure. Exploring different potential parameters and comparing the structures to those from unconstrained simulations and to experime... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5174730 Tue, 09 Aug 2011 23:00:00 +0100 5174730 http://www.medworm.com/index.php?rid=5174729&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%3D21864793%26dopt%3DAbstract In this study, molecular dynamics simulations were carried out on Lys- and Arg-containing Ala-based peptides (i.e. Ace-(AAAAK)(n)A-NH(2) and Ace-(AAAAR)(n)A-NH(2), where n=1-4), in order to explore and characterize their folding processes. For the oligopeptides, the evolution of α-helical structure with regard to the whole conformation, as well as to each residue was investigated, and the helix-forming propensities were characterized. On the basis of the helicity curves, representing the alteration of average helicity as a function of time, the typical time values describing the folding processes and subprocesses were identified. In the case of each peptide, the evolution and role of helix-stabilizing, non-local and side-chain-to-backbone H-bonds were examined. The appearing i←i+4 H-bon... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5174729 Tue, 09 Aug 2011 23:00:00 +0100 5174729 http://www.medworm.com/index.php?rid=5174728&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%3D21864794%26dopt%3DAbstract Authors: Chang Y, Sahinidis NV Abstract De novo sequence assembly is a ubiquitous combinatorial problem in all DNA sequencing technologies. In the presence of errors in the experimental data, the assembly problem is computationally challenging, and its solution may not lead to a unique reconstruct. The enumeration of all alternative solutions is important in drawing a reliable conclusion on the target sequence, and is often overlooked in the heuristic approaches that are currently available. In this paper, we develop an integer programming formulation and global optimization solution strategy to solve the sequence assembly problem with errors in the data. We also propose an efficient technique to identify all alternative reconstructs. When applied to examples of sequencing-by-hybri... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5174728 Tue, 09 Aug 2011 23:00:00 +0100 5174728 http://www.medworm.com/index.php?rid=5000802&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%3D21704257%26dopt%3DAbstract Authors: Wang D, Cheng L, Wang M, Wu R, Li P, Li B, Zhang Y, Gu Y, Zhao W, Wang C, Guo Z When using microarray data for studying a complex disease such as cancer, it is a common practice to normalize data to force all arrays to have the same distribution of probe intensities regardless of the biological groups of samples. The assumption underlying such normalization is that in a disease the majority of genes are not differentially expressed genes (DE genes) and the numbers of up- and down-regulated genes are roughly equal. However, accumulated evidences suggest gene expressions could be widely altered in cancer, so we need to evaluate the sensitivities of biological discoveries to violation of the normalization assumption. Here, we analyzed 7 large Affymetrix datasets of pair-matched n... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000802 Tue, 31 May 2011 23:00:00 +0100 5000802 http://www.medworm.com/index.php?rid=5000801&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%3D21704258%26dopt%3DAbstract In this study, the random forest models based on local sequence-structure features were proposed to identify miRNA in four species. The accuracies achieved were 86.51% for Homo sapiens, 81.66% for Ornithorhynchus anatinus, 82.33% for Mus musculus and 85.71% for Schmidtea mediterranea, respectively. Furthermore, the important analysis of feature elements was carried out by using the conditional feature importance strategy. The analysis results revealed that most of the significant elements were related to guanine-cytosine (GC) base pair. We believed that our method could be beneficial to annotate the function of miRNA and help the further understanding of the RNA interference mechanism. PMID: 21704258 [PubMed - in process] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000801 Tue, 31 May 2011 23:00:00 +0100 5000801 http://www.medworm.com/index.php?rid=5000800&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%3D21704259%26dopt%3DAbstract Authors: Hu G, Shen S, Wang K The methods of phylogenetic inference have become more and more realistic and effective since the evolution rate was taken into account. In order to study the evolution rate more comprehensively, all 13 protein coding genes in 123 mammalian mitochondrial genomes are analyzed. The evolution rates of different codon position are analyzed as well. The evolution rate is estimated by Shannon entropy. We find that the distribution of 3rd codon position doesn't follow gamma distribution and the results suggest that it follows a mixed distribution of gamma distribution and normal distribution. The relationship between different codon positions is also studied. We find that there are significant positive correlation between three codon positions. Especially between... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000800 Tue, 31 May 2011 23:00:00 +0100 5000800 http://www.medworm.com/index.php?rid=5000799&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%3D21704260%26dopt%3DAbstract Authors: Li M, Wang J, Chen X, Wang H, Pan Y Identifying essential proteins is very important for understanding the minimal requirements of cellular survival and development. Fast growth in the amount of available protein-protein interactions has produced unprecedented opportunities for detecting protein essentiality from the network level. Essential proteins have been found to be more abundant among those highly connected proteins. However, there exist a number of highly connected proteins which are not essential. By analyzing these proteins, we find that few of their neighbors interact with each other. Thus, we propose a new local method, named LAC, to determine a protein's essentiality by evaluating the relationship between a protein and its neighbors. The performance of LAC is vali... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000799 Tue, 31 May 2011 23:00:00 +0100 5000799 http://www.medworm.com/index.php?rid=5000798&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%3D21704261%26dopt%3DAbstract Authors: Wang Y, Chen J, Li Q, Wang H, Liu G, Jing Q, Shen B The development and diverse application of microarray and next generation sequencing technologies has made the meta-analysis widely used in expression data analysis. Although it is commonly accepted that pathway, network and systemic level approaches are more reproducible than reductionism analyses, the meta-analysis of prostate cancer associated molecular signatures at the pathway level remains unexplored. In this article, we performed a meta-analysis of 10 prostate cancer microarray expression datasets to identify the common signatures at both the gene and pathway levels. As the enrichment analysis result of GeneGo's database and KEGG database, 97.8% and 66.7% of the signatures show higher similarity at pathway level than t... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000798 Tue, 31 May 2011 23:00:00 +0100 5000798 http://www.medworm.com/index.php?rid=5000797&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%3D21704262%26dopt%3DAbstract Authors: Anselmi C, Buonocore A, Centini M, Facino RM, Hatt H To gain structural insight on the interactions between odorants and the human olfactory receptor, we did homology modelling of the receptor structure, followed by molecular docking simulation with ligands. Molecular dynamics simulation on the structures resulting from docking served to estimate the binding free energy of the various odorant families. A correlation with the odorous properties of the ligands is proposed. We also investigated which residues were involved in the binding of a set of properly synthesised ligands and which were required for fitting inside the binding pocket. Olfactive stimulation of the olfactory receptor with odorous molecules was also investigated, using calcium imaging or electrophysiological re... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000797 Tue, 31 May 2011 23:00:00 +0100 5000797 http://www.medworm.com/index.php?rid=5000796&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%3D21704263%26dopt%3DAbstract Authors: Zhou R, He Y, Xiao Y At present we have already had the detailed knowledge of the folding of small model proteins, but a unified picture of how large proteins fold is still absent. We simulated the folding of a large eight-helix-bundle protein with a length of 145 amino acids by using a united-residue protein model. We observed a multiple nucleation folding pathway: the formation of secondary structures was followed by the nucleation of helices at the two terminal parts and also at the middle of the chain, and then the nuclei grew and combined with each other to form the tertiary structure. Surprisingly, we also found a vectorial folding pathway that was shown recently for co-translational folding in the ribosome exit tunnel. Furthermore, we found that all three-helix subunits... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000796 Tue, 31 May 2011 23:00:00 +0100 5000796 http://www.medworm.com/index.php?rid=5000795&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%3D21704264%26dopt%3DAbstract Authors: Hollup SM, Sadowski MI, Jonassen I, Taylor WR Protein structure comparison by pairwise alignment is commonly used to identify highly similar substructures in pairs of proteins and provide a measure of structural similarity based on the size and geometric similarity of the match. These scores are routinely applied in analyses of protein fold space under the assumption that high statistical significance is equivalent to a meaningful relationship, however the truth of this assumption has previously been difficult to test since there is a lack of automated methods which do not rely on the same underlying principles. As a resolution to this we present a method based on the use of topological descriptions of global protein structure, providing an independent means to assess the abil... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000795 Tue, 31 May 2011 23:00:00 +0100 5000795 http://www.medworm.com/index.php?rid=5000794&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%3D21704265%26dopt%3DAbstract Authors: Yang Y, Li Z, Nan P, Zhang X Glucose-6-phosphate dehydrogenase (G6PD) is an essential enzyme that protects human red blood cells from premature destruction caused by oxidative damage. People suffering from G6PD deficiency would be vulnerable to various oxidative substances, such as fava beans and oxidant drugs. Until now, many institutes, organizations or domain experts have compiled low-risk or high-risk drugs collection for patients with G6PD deficiency, mainly from the case report or clinical trails. Recently, we have explored a classification system to predict drug-induced hemolytic potential. In this paper, we screen the normally used over-the-counter (OTC) drugs for "high-risk" and "low-risk" ones to G6PD deficient patients by this system. PMID: 21704265 [PubMed - in... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000794 Tue, 31 May 2011 23:00:00 +0100 5000794 http://www.medworm.com/index.php?rid=5000793&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%3D21704266%26dopt%3DAbstract Authors: Wang B, Hou B, Xing F, Yao Y The spatial stochastic simulation of biochemical systems requires significant calculation efforts. Parallel discrete-event simulation is a promising approach to accelerate the execution of simulation runs. However, achievable speedup depends on the parallelism inherent in the model. One of our goals is to explore this degree of parallelism in the Next Subvolume Method type simulations. Therefore we introduce the Abstract Next Subvolume Method, in which we decouple the model representation from the sequential simulation algorithms, and prove that state trajectories generated by its executions statistically accord with those generated by the Next Subvolume Method. The experimental performance analysis shows that optimistic synchronization algorithms,... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000793 Tue, 31 May 2011 23:00:00 +0100 5000793 http://www.medworm.com/index.php?rid=5000792&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%3D21704267%26dopt%3DAbstract Authors: Garbarine E, Depasquale J, Gadia V, Polikar R, Rosen G Analysis of DNA sequences isolated directly from the environment, known as metagenomics, produces a large quantity of genome fragments that need to be classified into specific taxa. Most composition-based classification methods use all features instead of a subset of features that may maximize classifier accuracy. We show that feature selection methods can boost performance of taxonomic classifiers. This work proposes three different filter-based feature selection methods that stem from information theory: (1) a technique that combines Kullback-Leibler, Mutual Information, and distance information, (2) a text mining technique, TF-IDF, and (3) minimum redundancy-maximum-relevance (mRMR). The feature selection methods are co... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=5000792 Tue, 31 May 2011 23:00:00 +0100 5000792 http://www.medworm.com/index.php?rid=4954491&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%3D21666777%26dopt%3DAbstract Authors: Xia J, Sun J, Jia P, Zhao Z Protein-protein interaction (PPI) network analysis has been widely applied in the investigation of the mechanisms of diseases, especially cancer. Recent studies revealed that cancer proteins tend to interact more strongly than other categories of proteins, even essential proteins, in the human interactome. However, it remains unclear whether this observation was introduced by the bias towards more cancer studies in humans. Here, we examined this important issue by uniquely comparing network characteristics of cancer proteins with three other sets of proteins in four organisms, three of which (fly, worm, and yeast) whose interactomes are essentially not biased towards cancer or other diseases. We confirmed that cancer proteins had stronger connectivi... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4954491 Tue, 31 May 2011 23:00:00 +0100 4954491 http://www.medworm.com/index.php?rid=4855855&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%3D21555249%26dopt%3DAbstract Discussions on Reverse Engineering Assessment and Methods) 2009 Challenge consists of predicting a position weight matrix (PWM) that describes the specificity profile of five PDZ domains to their target peptides. We consider the primary structures of each of the five PDZ domains as a numerical sequence derived from graph-theoretic models of each of the individual amino acids in the protein sequence. Using available PDZ domain databases to obtain known targets, the graph-theoretic based numerical sequences are then used to train a neural network to recognize their targets. Given the challenge sequences, the target probabilities are computed and a corresponding position weight matrix is derived. In this work we present our method. The results of our method placed second in the DREAM 2009 cha... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4855855 Thu, 31 Mar 2011 23:00:00 +0100 4855855 http://www.medworm.com/index.php?rid=4750285&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%3D21514893%26dopt%3DAbstract Authors: Niranjan Reddy BP, Prasad GB, Raghavendra K The availability of whole genome sequence information of Ixodes scapularis (Acari: Ixodidae), an important disease vector of veterinary and public health importance, has opened up new opportunities to explore the vector species at genomic level. Use of acaricides is the mainstay in controlling the disease vector, as effective vaccines are not available for most of the diseases that are transmitted by ticks. The glutathione S-transferase (GST) enzymes are one of the important supergene families that are involved in protecting the organism from oxidative stress and xenobiotics including the acaricides. The analysis of GST supergene family from Ixodes identified all the three broad GST classes, viz. canonical, mitochondrial, and microso... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4750285 Thu, 31 Mar 2011 23:00:00 +0100 4750285 http://www.medworm.com/index.php?rid=4750286&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%3D21482193%26dopt%3DAbstract Authors: Khatibisepehr S, Huang B, Ibrahim F, Xing JZ, Roa W This paper is concerned with dynamic modeling, prediction and analysis of cell cytotoxicity induced by water contaminants. A real-time cell electronic sensing (RT-CES) system has been used for continuously monitoring dynamic cytotoxicity responses of living cells. Cells are grown onto the surfaces of the microelectronic sensors. Changes in cell number expressed as cell index (CI) have been recorded on-line as time series. The CI data are used to develop dynamic prediction models for cell cytotoxicity process. We consider support vector regression (SVR) algorithm to implement data-based system identification for dynamic modeling and prediction of cytotoxicity. Through several validation studies, multi-step-ahead predictions ar... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4750286 Wed, 16 Mar 2011 00:00:00 +0100 4750286 http://www.medworm.com/index.php?rid=4697409&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%3D21470914%26dopt%3DAbstract Authors: Seligmann H Codon-anticodon mismatches and tRNA misloadings cause translational amino acid misinsertions, producing dysfunctional proteins. Here I explore the original hypothesis whether mismatches tend to compensate misacylation, so as to insert the amino acid coded by the codon. This error compensation is promoted by the fact that codon-anticodon mismatch stabilities increase with tRNA misacylation potentials (predicted by 'tfam') by non-cognate amino acids coded by the mismatched codons for most tRNAs examined. Error compensation is independent of preferential misacylation by non-cognate amino acids physico-chemically similar to cognate amino acids, a phenomenon that decreases misinsertion impacts. Error compensation correlates negatively with (a) codon/anticodon abundance ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4697409 Wed, 16 Mar 2011 00:00:00 +0100 4697409 http://www.medworm.com/index.php?rid=4578489&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%3D21353643%26dopt%3DAbstract Authors: Rao RS, Buus OT, Wollenweber B N-glycosylation is a common protein modification process, which affects a number of properties of proteins. Little is known about the distribution of N-glycosylation sequons, for example, the distance between glycosylated sites and their position in the protein primary sequence. Using a large set of experimentally confirmed eukaryotic N-glycoproteins we analyzed the relative position and distribution of sequons. N-Glycosylation probability was found to be lower in the termini of protein sequences compared to the mid region. N-glycosylated sequons were found much farther from C terminus compared to the N-terminus of the protein sequence and this effect was more pronounced for NXS sequons. The distribution of sequons, modeled based on balls-in-boxe... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4578489 Wed, 02 Feb 2011 00:00:00 +0100 4578489 http://www.medworm.com/index.php?rid=4525281&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%3D21349769%26dopt%3DAbstract Authors: Jiao QJ, Huang Y, Shen HB Research on gene co-expression not only plays an important role in understanding the complex regulatory relationships, but also contributes to our understanding of gene regulatory network. Beyond the co-expression knowledge between two genes, investigating the co-expression relationships among multiple target genes is more informative for understanding the basic working mechanisms in a cell. In this paper, all the Arabidopsis anther genes and every gene's potential co-expressed partners are collected by cross-database search. By combining simple pair gene co-expression networks, a complex Arabidopsis anther co-expression network is constructed. Maximum-clique algorithm is then applied to mine the groups reflecting co-expression relationships among mul... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4525281 Wed, 02 Feb 2011 00:00:00 +0100 4525281 http://www.medworm.com/index.php?rid=4525282&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%3D21333602%26dopt%3DAbstract We present a simple formula for calculating effective sample size for many types of relative pairs and relative sets. For allele frequency estimation, the effective sample size method captures the variance inflation exactly. For genotype frequency, simulations showed that effective sample size provides a satisfactory approximation. A gene which is previously identified as a type 1 diabetes susceptibility locus, the interferon-induced helicase gene (IFIH1), is shown to be significantly associated with rheumatoid arthritis when the effective sample size method is applied. This significant association is not established if only one affected sib per pedigree were used in the association analysis. Relationship between the effective sample size method and other methods - the generalized estimati... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4525282 Sat, 22 Jan 2011 00:00:00 +0100 4525282 http://www.medworm.com/index.php?rid=4525283&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%3D21320803%26dopt%3DAbstract Authors: Zhang JL, Zheng QC, Zhang HX The selectivity of a known arylsulfonamides inhibitor for two isozymes II and VII of human carbonic anhydrases (hCAs) was studied by homology modeling, molecular docking and molecular dynamics methods. The results show that the selectivity of the inhibitor for two isozymes is due to the different side chain lengths between N67 of hCA II and Q64 of hCA VII. One more methene group in the side chain of Q64 of hCA VII makes it possible to form the hydrogen bond with the bromide atom of the known inhibitor. From the point of view, the modification to the known inhibitor was performed to obtain an inhibitor with higher selectivity. The complex conformations of the new designed inhibitor and two isozymes designate the formation of the hydrogen bond betwee... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4525283 Fri, 21 Jan 2011 00:00:00 +0100 4525283 http://www.medworm.com/index.php?rid=4525284&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%3D21317044%26dopt%3DAbstract Authors: Ng KM, Solayappan M, Poh KL This paper presents an interior point method to determine the minimum energy conformation of alanine dipeptide. The CHARMM energy function is minimized over the internal coordinates of the atoms involved. A barrier function algorithm to determine the minimum energy conformation of peptides is proposed. Lennard-Jones 6-12 potential which is used to model the van der Waals interactions in the CHARMM energy equation is used as the barrier function for this algorithm. The results of applying the algorithm for the alanine dipeptide structure as a function of varying number of dihedral angles are reported, and they are compared with that obtained from genetic algorithm approach. In addition, the results for polyalanine structures are also reported. PM... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4525284 Wed, 19 Jan 2011 00:00:00 +0100 4525284 http://www.medworm.com/index.php?rid=4525285&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%3D21315656%26dopt%3DAbstract Authors: Shortridge MD, Triplet T, Revesz P, Griep MA, Powers R Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4525285 Tue, 18 Jan 2011 00:00:00 +0100 4525285 http://www.medworm.com/index.php?rid=4470633&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%3D21310660%26dopt%3DAbstract Authors: Levtsova OV, Antonov MY, Naumenkova TV, Sokolova OS In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the interaction with the prokaryotic membrane zervamicin placed by its N-termini towards the lipids and rotated at an angle of 40° relatively to the bilayer surface. In the case of eukaryotic membrane zervamicin stayed in the water and located parallel to the membrane surface. We compared hydrogen bonds between peptide and lipids and concluded that interactions of ZrvIIB with prokaryotic membrane are stronger than those ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4470633 Wed, 05 Jan 2011 00:00:00 +0100 4470633 http://www.medworm.com/index.php?rid=4400197&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%3D21247808%26dopt%3DAbstract Authors: Chen Y, Yan X, Chen S Glucosinolates constitute a major group of secondary metabolites in Arabidopsis, which play an important role in plant interaction with pathogens and insects. Advances in glucosinolate research have defined the biosynthetic pathways. However, cross-talk and interaction between glucosinolate pathway and other molecular pathways are largely unknown. Here three bioinformatics tools were used to explore novel components and pathway connections in glucosinolate network. Although none of the software tools were prefect to predict glucosinolate genes, combination of results generated by all the tools led to successful prediction of all known glucosinolate genes. This approach was used to predict new genes in glucosinolate network. A total of 330 genes were found... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4400197 Thu, 23 Dec 2010 00:00:00 +0100 4400197 http://www.medworm.com/index.php?rid=4333891&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%3D21216672%26dopt%3DAbstract Authors: Kavousi K, Moshiri B, Sadeghi M, Araabi BN, Moosavi-Movahedi AA Protein function is related to its chemical reaction to the surrounding environment including other proteins. On the other hand, this depends on the spatial shape and tertiary structure of protein and folding of its constituent components in space. The correct identification of protein domain fold solely using extracted information from protein sequence is a complicated and controversial task in the current computational biology. In this article a combined classifier based on the information content of extracted features from the primary structure of protein has been introduced to face this challenging problem. In the first stage of our proposed two-tier architecture, there are several classifiers each of which is... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4333891 Fri, 17 Dec 2010 00:00:00 +0100 4333891 http://www.medworm.com/index.php?rid=4217785&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%3D21106461%26dopt%3DAbstract Authors: Sahu SS, Panda G During last few decades accurate determination of protein structural class using a fast and suitable computational method has been a challenging problem in protein science. In this context a meaningful representation of a protein sample plays a key role in achieving higher prediction accuracy. In this paper based on the concept of Chou's pseudo amino acid composition (Chou, K.C., 2001. Proteins 43, 246-255), a new feature representation method is introduced which is composed of the amino acid composition information, the amphiphilic correlation factors and the spectral characteristics of the protein. Thus the sample of a protein is represented by a set of discrete components which incorporate both the sequence order and the length effect. On the basis of such ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4217785 Wed, 01 Dec 2010 00:00:00 +0100 4217785 http://www.medworm.com/index.php?rid=4139535&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%3D21036669%26dopt%3DAbstract Authors: Ibraheem O, Botha CE, Bradley G The regulation of gene expression involves a multifarious regulatory system. Each gene contains a unique combination of cis-acting regulatory sequence elements in the 5' regulatory region that determines its temporal and spatial expression. Cis-acting regulatory elements are essential transcriptional gene regulatory units; they control many biological processes and stress responses. Thus a full understanding of the transcriptional gene regulation system will depend on successful functional analyses of cis-acting elements. Cis-acting regulatory elements present within the 5' regulatory region of the sucrose transporter gene families in rice (Oryza sativa Japonica cultivar-group) and Arabidopsis thaliana, were identified using a bioinformatics app... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4139535 Fri, 29 Oct 2010 00:00:00 +0100 4139535 http://www.medworm.com/index.php?rid=4123095&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%3D21030312%26dopt%3DAbstract In this study, we carried out functional analyses of sRNAs from 26 angiosperms by utilizing public sRNA NGS data. We proposed that the endogenous sRNAs largely represented by the 24-nt ones had a potential role in transposable element (TE) control in both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), based on the comparison of sRNA locus densities within the TEs to the non-TE genes. Functional analysis was performed for the predicted targets of the conserved sRNAs that were classified into eudicot-specific, monocot-specific, and angiosperm-conserved ones. Moreover, several miRNA families were found to be highly conserved, and miR396 was suggested to be the most conserved miRNA family between the eudicots and the monocots, indicating its essential role in angiosperm developmen... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4123095 Tue, 26 Oct 2010 00:00:00 +0100 4123095 http://www.medworm.com/index.php?rid=4123096&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%3D20980202%26dopt%3DAbstract Authors: Płoński P, Radomski JP Ever increasing amounts of genetic information stored in sequential databases require efficient methods to automatically reveal their phylogenetic relationships. A framework for in silico unambiguous analysis of phylogenetic trees, based on information contained in tree's topology, together with its branches length, is proposed. The resulting, translated tree has all nodes labeled, with no constraints on nodes' degree, and the subsequent finding of evolutionary pathways from the QPF-translated tree is robust and straightforward. Main features of the method are: small demands on computational time, and the ability to analyze phylogenies obtained prior to the proposed QPF analysis by any traditional tree-building technique. PMID: 20980202 [PubMed - a... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4123096 Mon, 25 Oct 2010 00:00:00 +0100 4123096 http://www.medworm.com/index.php?rid=4123094&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%3D21030313%26dopt%3DAbstract In this study, we applied a computational approach to analyze expressed sequence tags, and identified 32 miRNAs belonging to 22 miRNA families, in three earthworm species Eisenia fetida, Eisenia andrei, and Lumbricus rubellus. These newly identified earthworm miRNAs possess a difference of 2-4 nucleotides from their homologous counterparts in Caenorhabditis elegans. They also share similar features with other known animal miRNAs, for instance, the nucleotide U being dominant in both mature and pre-miRNA sequences, particularly in the first position of mature miRNA sequences at the 5' end. The newly identified earthworm miRNAs putatively regulate mRNA genes that are involved in many important biological processes and pathways related to development, growth, locomotion, and reproduction as w... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4123094 Thu, 07 Oct 2010 00:00:00 +0100 4123094 http://www.medworm.com/index.php?rid=4088255&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%3D20951093%26dopt%3DAbstract Authors: Reker D, Katzenbeisser S, Hamacher K Understanding evolution at the sequence level is one of the major research visions of bioinformatics. To this end, several abstract models - such as Hidden Markov Models - and several quantitative measures - such as the mutual information - have been introduced, thoroughly investigated, and applied to several concrete studies in molecular biology. With this contribution we want to undertake a first step to merge these approaches (models and measures) for easy and immediate computation, e.g. for a database of a large number of externally fitted models (such as PFAM). Being able to compute such measures is of paramount importance in data mining, model development, and model comparison. Here we describe how one can efficiently compute the mutu... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4088255 Tue, 21 Sep 2010 23:00:00 +0100 4088255 http://www.medworm.com/index.php?rid=4088254&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%3D20952258%26dopt%3DAbstract Authors: Lèbre S, Michel CJ We develop here a new class of stochastic models of gene evolution based on residue Insertion-Deletion Independent from Substitution (IDIS). Indeed, in contrast to all existing evolution models, insertions and deletions are modeled here by a concept in population dynamics. Therefore, they are not only independent from each other, but also independent from the substitution process. After a separate stochastic analysis of the substitution and the insertion-deletion processes, we obtain a matrix differential equation combining these two processes defining the IDIS model. By deriving a general solution, we give an analytical expression of the residue occurrence probability at evolution time t as a function of a substitution rate matrix, an insertion rate vector... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4088254 Thu, 16 Sep 2010 23:00:00 +0100 4088254 http://www.medworm.com/index.php?rid=4042423&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%3D20884298%26dopt%3DAbstract Authors: Zorkoltseva IV, Aulchenko YS, van Duijn CM, Axenovich TI A high-throughput resequencing technology has brought family based studies back into genetic research focus. Within-family outliers (the individuals whose phenotype is very much unlike the phenotype of relatives) may carry rare variants of large effects and thus resequencing of these provides a highly powered strategy for rare variants detection. On the other hand, such outliers may complicate search for common variants of smaller effects, because they may obscure a real linkage signal. We have developed a program Ped_Outlier allowing automatic detection of within-family outliers in a sample of pedigrees of arbitrary structure and size. We tested our program by identification of within-family outliers for adult height an... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4042423 Wed, 08 Sep 2010 23:00:00 +0100 4042423 http://www.medworm.com/index.php?rid=4042422&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%3D20888301%26dopt%3DAbstract In this study, we tested our algorithm in 11 microarray datasets for brain, leukemia, lung, prostate, and others. We show that the proposed swarm intelligence algorithm successfully increase the classification accuracy and decrease the number of selected features compared to other swarm intelligence methods. PMID: 20888301 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4042422 Wed, 08 Sep 2010 23:00:00 +0100 4042422 http://www.medworm.com/index.php?rid=4042421&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%3D20889382%26dopt%3DAbstract Authors: Kanth BK, Liou K, Sohng JK Homology models of cytochrome P450 105P2 (CYP105P2) were constructed using four P450 structures, CYP105A1, CYP105, CYP165B3 and CYP107L1, as templates for the model building. Using Accelrys Discovery Studio 2.1 software, the lowest energy CYP105P2 model was then assessed for stereochemical quality and side-chain environment. Further active site optimization of the CYP105P2 model built using these templates was performed by molecular dynamics to generate the final CYP105P2 model. The substrates, flavone, flavanone, quercetin and naringenin, were docked into the model. The model-flavone complex was used to validate the active site architecture, and structurally and functionally important residues were identified by subsequent characterization of the se... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4042421 Mon, 23 Aug 2010 23:00:00 +0100 4042421 http://www.medworm.com/index.php?rid=4003611&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%3D20863765%26dopt%3DAbstract In conclusion, ps-miRNAs may play critical roles in differentiation and growth regulation during early development, especially in maintaining the pluripotency of hESCs. Results from this study may help explaining the differences between primates and lower vertebrates at genetic level. PMID: 20863765 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=4003611 Mon, 23 Aug 2010 23:00:00 +0100 4003611 http://www.medworm.com/index.php?rid=3865548&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%3D20702140%26dopt%3DAbstract Authors: He Z, Yu W Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this article, we review existing stable feature selection methods for biomarker discovery using a generic hierarchical framework. We have two objectives: (1) providing an overview on this new yet fast growing topic for a convenient reference; (2) categorizing existing methods under an expandable framework for future research and development. PMID: 20702140 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3865548 Sun, 08 Aug 2010 23:00:00 +0100 3865548 http://www.medworm.com/index.php?rid=3777382&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%3D20637698%26dopt%3DAbstract In this study, we tested by computational and statistical approaches if the exonic splicing enhancer motif binding to the SF2/ASF SR protein is conserved among several groups of human genes. The results showed that the SF2/ASF ESE consensus was conserved between genes within the same chromosome, within different chromosomes and between different levels of muscular cells differentiation. However, this motif displays subtle variations within the consensus sequence between genes expressed in different tissues. These results can emphasize the presence of different translational isoforms of the SFRS1 gene encoding for the SF2/ASF, or different post-translational protein maturations in different tissues. This tissular discrepancy can also account for the alternative splicing of several genes bet... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3777382 Thu, 24 Jun 2010 23:00:00 +0100 3777382 http://www.medworm.com/index.php?rid=3777381&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%3D20643583%26dopt%3DAbstract Authors: Schneckener S, Görlitz L, Ellinger-Ziegelbauer H, Ahr HJ, Schuppert A Exposing eukaryotic cells to a toxic compound and subsequent gene expression profiling may allow the prediction of selected toxic effects based on changes in gene expression. This objective is complicated by the observation that compounds with different modes of toxicity cause similar changes in gene expression and that a global stress response affects many genes. We developed an elastic network model of global stress response with nodes representing genes which are connected by edges of graded coexpression. The expression of only few genes have to be known to model the global stress response of all but a few atypical responder genes. Those required genes and the atypical response genes are shown to be go... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3777381 Thu, 24 Jun 2010 23:00:00 +0100 3777381 http://www.medworm.com/index.php?rid=3750343&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%3D20621565%26dopt%3DAbstract Authors: Joo H, Qu X, Swanson R, McCallum CM, Tsai J In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone varphi,psi angles with the first side-chain torsion angles (chi(1)) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain e... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3750343 Fri, 18 Jun 2010 23:00:00 +0100 3750343 http://www.medworm.com/index.php?rid=3750345&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%3D20619742%26dopt%3DAbstract Authors: Burguillo FJ, Martin J, Barrera I, Bardsley WG With the proliferation of related microarray studies by independent groups, a natural approach to analysis would be to combine the results across studies. In this article, we address a meta-analysis of the gene expression data on imatinib resistance in chronic myelogenous leukemia. First, an analysis of the overlapping among 6 published studies revealed that only 3 genes were coincident between 2 studies. A later reprocessing using different methods on 4 publicly available datasets revealed that 2 extra genes were overlapped between two sets. Both poor overlappings may be due to large differences in the sample source, the microarray platforms used, and a small difference in gene expression between the imatinib non-responder and re... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3750345 Thu, 17 Jun 2010 23:00:00 +0100 3750345 http://www.medworm.com/index.php?rid=3750344&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%3D20619743%26dopt%3DAbstract In this study, we present a global relative expression analysis of miRNAs in human miRNA gene cluster and family based on different selection schemes of isomiRs from deep sequencing data. Some divergence was observed between expression distributions based on sequence count of the most abundant isomiR and sum of all isomiR sequence counts, respectively. But the divergence showed less effect on expression patterns in miRNA gene cluster and family. Because of high sensitivity of sequencing technology and ambiguous distribution of common isomiRs among multicopy miRNA precursors and homologous genes, most gene clusters and families showed inconsistent expression levels. Inconsistent expression pattern implied expression diversification in vivo although they maybe showed close relationship durin... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3750344 Thu, 17 Jun 2010 23:00:00 +0100 3750344 http://www.medworm.com/index.php?rid=3734068&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%3D20598639%26dopt%3DAbstract We present a modular, collaborative, open-source architecture for rigid body modelling based upon small angle scattering data, named sas_rigid. It is designed to provide a fast and extensible scripting interface using the easy-to-learn Python programming language. Features include rigid body modelling to result in static structures and three-dimensional probability densities using two different algorithms. PMID: 20598639 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3734068 Tue, 01 Jun 2010 23:00:00 +0100 3734068 http://www.medworm.com/index.php?rid=3655859&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%3D20537955%26dopt%3DAbstract Authors: Goonesekere NC, Shipely K, O'Connor K The Pfam database is an important tool in genome annotation, since it provides a collection of curated protein families. However, a subset of these families, known as domains of unknown function (DUFs), remains poorly characterized. We have related sequences from DUF404, DUF407, DUF482, DUF608, DUF810, DUF853, DUF976 and DUF1111 to homologs in PDB, within the midnight zone (9-20%) of sequence identity. These relationships were extended to provide functional annotation by sequence analysis and model building. Also described are examples of residue plasticity within enzyme active sites, and change of function within homologous sequences of a DUF. PMID: 20537955 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemis... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3655859 Mon, 24 May 2010 23:00:00 +0100 3655859 http://www.medworm.com/index.php?rid=3655860&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%3D20537588%26dopt%3DAbstract Authors: Ribeiro AS, Häkkinen A, Healy S, Yli-Harja O We study how long pause-prone sites, commonly sequence-dependent, affect transcription and RNA temporal levels in a delayed stochastic model of transcription at the single nucleotide level. We vary pause propensity, duration and the probability of premature termination of elongation at the pause site. We also study the effects of multiple pause sites. We show that pause sites can be used to fine-tune noise strength and burst size distribution of RNA levels. Varying pause rate and duration alone affects bursting but noise is not significantly affected. Noise strength can be changed by varying both parameters and, even more pronouncedly, by varying the probability of premature termination. Adding multiple pause sites amplifies the ... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3655860 Sat, 08 May 2010 23:00:00 +0100 3655860 http://www.medworm.com/index.php?rid=3522014&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%3D20427241%26dopt%3DAbstract Authors: Durrant JD, McCammon JA Pandemic (H1N1) influenza poses an imminent threat. Nations have stockpiled inhibitors of the influenza protein neuraminidase in hopes of protecting their citizens, but drug-resistant strains have already emerged, and novel therapeutics are urgently needed. In the current work, the computer program AutoGrow is used to generate novel predicted neuraminidase inhibitors. Given the great flexibility of the neuraminidase active site, protein dynamics are also incorporated into the computer-aided drug-design process. Several potential inhibitors are identified that are predicted to bind to neuraminidase better than currently approved drugs. PMID: 20427241 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3522014 Fri, 02 Apr 2010 23:00:00 +0100 3522014 http://www.medworm.com/index.php?rid=3522012&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%3D20430699%26dopt%3DAbstract Authors: Hu J, Li H, Zhang J Transcriptional regulation in eukaryotic genes generally requires combinatorial binding on DNA of multiple transcription factors. Though many analyses have been performed for identification of combinatorial patterns in promoter sequences, there are few studies concerned with introns of genes. Here our study focuses on the transcriptional synergistic (cooperative) regulation between upstream promoters and introns of ribosomal protein (RP) genes in Saccharomyces cerevisiae yeast. We first extract some potential transcriptional regulatory motifs based on a statistical comparative analysis. 98% of these motifs are accordance with experimental analyses. Then by pairing these motifs each other, we identify some potential synergistic motif pairs between upstream r... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3522012 Fri, 02 Apr 2010 23:00:00 +0100 3522012 http://www.medworm.com/index.php?rid=3522011&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%3D20430700%26dopt%3DAbstract Authors: Sabarinathan R, Basu R, Sekar K The occurrence of similar structural repeats in a protein structure has evolved through gene duplication. These repeats act as a structural building block and form more than one compact structural and functional unit called a repeat domain. The protein families comprising similar structural repeats are mainly involved in protein-protein interactions as well as binding to other ligand molecules. The identification of internal sequence repeats in the primary structure is not sufficient for the analysis of structural repeats. Thus, a new method called ProSTRIP has been developed using dynamic programming to find the similar structural repeats in a three-dimensional protein structure. The detection of these repeats is made by calculating the protein... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3522011 Fri, 02 Apr 2010 23:00:00 +0100 3522011 http://www.medworm.com/index.php?rid=3522013&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%3D20427242%26dopt%3DAbstract Authors: Michel CJ, Pirillo G A new trinucleotide proposition is proved here and allows all the trinucleotide circular codes on the genetic alphabet to be identified (their numbers and their sets of words). This new class of genetic motifs, i.e. circular codes (or synchronizing genetic motifs), may be involved in the structure and the origin of the genetic code, and in reading frames of genes. PMID: 20427242 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry) Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3522013 Sat, 27 Mar 2010 00:00:00 +0100 3522013 http://www.medworm.com/index.php?rid=3468128&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%3D20381428%26dopt%3DAbstract Authors: Pienaar E, Fluitt AM, Whitney SE, Freifeld AG, Viljoen HJ The model herein aims to explore the dynamics of the spread of tuberculosis (TB) in an informal settlement or township. The population is divided into households of various sizes and also based on commuting status. The model dynamics distinguishes between three distinct social patterns: the exposure of commuters during travel, random diurnal interaction and familial exposure at night. Following the general SLIR models, the population is further segmented into susceptible (S), exposed/latently infected (L), active/infectious (I), and recovered (R) individuals. During the daytime, commuters travel on public transport, while non-commuters randomly interact in the community to mimic chance encounters with infectious persons... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3468128 Tue, 09 Mar 2010 00:00:00 +0100 3468128 http://www.medworm.com/index.php?rid=3420870&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%3D20347393%26dopt%3DAbstract Authors: Waligórski P, Szaleniec M Self-incompatibility (SI) of white cabbage (Brassica oleracea var. capitata), a biological mechanism triggering the ability to pollinate plant ovules, is modelled based on the statistical analysis of electrophoretic patterns of stigma extracts. The patterns obtained for 72 plants grown in three different seasons (2003-2005) have been explored with discriminant analysis and non-linear neural networks. The NN models obtained perform a flawless classification of SI and provide a useful and fast technique for SI prediction before the end of the season. The discriminant analysis turns out to be less effective (74% of good predictions), but together with sensitivity analysis of NN, it points out the important markers of the SI process (peaks 1, 3, 5, 1... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3420870 Tue, 09 Mar 2010 00:00:00 +0100 3420870 http://www.medworm.com/index.php?rid=3420869&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%3D20347394%26dopt%3DAbstract Authors: Seligmann H Off frame reading of protein coding sequences reveals numerous stop codons. The genetic code and genomic codon usages maximize hidden stop numbers, minimizing effects of ribosomal slippages. This increases efficiency and homogeneity of protein expression. Here I test whether developmental stability in bilateral morphological traits of lizards and primates increases with numbers of hidden stops in mitochondrial protein coding genes. Expected effects are weak, but are apparent in 14 among 16 independent taxonomic groups for the non-coding +1 frame, and 12 among 16 for the -1 frame. Results stress that many molecular factors determine phenotypes in a complex manner, frequently undetectable by classical quantitative genetics. Explicit molecular hypotheses can partially... Computational Biology and Chemistry journals http://www.medworm.com/rss/comments.php?id=3420869 Tue, 09 Mar 2010 00:00:00 +0100 3420869 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 On "A comment on 'Prediction of protein structural classes by a new measure of information discrepancy"' Comput Biol Chem. 2009 Sep 16; 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