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 'In Silico Biol' source. Thu, 03 Dec 2009 15:57:37 +0100 http://www.medworm.com/index.php?rid=2858582&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795565%26dopt%3DAbstract Authors: Zhang W, Huang RS, Duan S, Dolan ME Men and women differ not only in their physical attributes and reproductive functions but also in many other characteristics, including the risks for some diseases as well as response to certain therapeutic treatments. Though genetically-identical for autosomal chromosomes, males and females could have gender-specific transcriptional or translational regulation, leading to differential mRNAs or protein products for some genes. To illustrate the gender-specific differences in mRNA-level expression, we compared gene expression patterns between males and females using a whole-genome microarray dataset on the unrelated HapMap lymphoblastoid cell lines derived from individuals of European (58 individuals) and African (59 individuals) ancestry. We... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858582 Sun, 04 Oct 2009 18:16:03 +0100 2858582 http://www.medworm.com/index.php?rid=2858581&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795566%26dopt%3DAbstract Authors: Synnergren J, Olsson B, Gamalielsson J Biological systems are extremely complex and often involve thousands of interacting components. Despite all efforts, many complex biological systems are still poorly understood. However, over the past few years high-throughput technologies have generated large amounts of biological data, now requiring advanced bioinformatic algorithms for interpretation into valuable biological information. Due to these high-throughput technologies, the study of biological systems has evolved from focusing on single components (e.g. genes) to encompassing large sets of components (e.g. all genes in an entire genome), with the aim to elucidate their interdependences in various biological processes. In addition, there is also an increasing need for integrat... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858581 Sun, 04 Oct 2009 18:16:03 +0100 2858581 http://www.medworm.com/index.php?rid=2858580&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795567%26dopt%3DAbstract Authors: Nandy A, Ghoshb A, Nandy P We propose a new method to compare sequences of protein families by generating numerical characterizations through a 20D representation. Using a walk along the axes representing the amino acids we generate a vector for each sequence whose components can be used to derive distance matrices between sequences and whose magnitudes can be used to compare the similarities/dissimilarities between the different sequences. The distance matrices enable creation of phylogenetic trees without need for multiple alignments or any other model dependencies. In this paper we test this technique with human globin gene sequences and then apply the method to a contemporary issue of evolutionary relationships of rat and human voltage-gated sodium channel alpha subunits a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858580 Sun, 04 Oct 2009 18:16:03 +0100 2858580 http://www.medworm.com/index.php?rid=2858579&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795568%26dopt%3DAbstract Authors: Wieser D, Niranjan M Distant evolutionary relationships between proteins with low sequence similarity are difficult to recognise by computational methods. Consequently, many sequences obtained from large-scale sequencing projects cannot be assigned to any known proteins or families despite being evolutionarily related. To boost sensitivity, various sequence-based methods have been modified to make use of the better conserved secondary structure. Most of these methods are instance-based or generative. Here, we introduce a kernel-based remote homology detection method that allows for a combination of sequence and secondary-structure similarity scores in a discriminative approach. We studied the ability of the method to predict superfamily membership as defined by the SCOP databa... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858579 Sun, 04 Oct 2009 18:16:03 +0100 2858579 http://www.medworm.com/index.php?rid=2858578&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795569%26dopt%3DAbstract Authors: Khan MT, Sylte I Naturally occurring peptidases from organisms living under extreme conditions are adapted to function in environmental extremes, including temperature, salinity, pH, or pressure. These organisms represent unique sources for new bio-molecules that have both industrial and medicinal application. Adaptive strategies for functioning under extreme conditions are reflected at the enzyme sequence and structural level. Understanding the determinants responsible for unique functional features can be used to enhance the functional features of known proteins. In the present study, the amino acid sequences of 81 peptidases of the thermolysin (M4) family were analyzed for possible determinants of psychrophilic and thermophilic features, by comparing with thermolysin from B... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858578 Sun, 04 Oct 2009 18:16:03 +0100 2858578 http://www.medworm.com/index.php?rid=2858577&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795570%26dopt%3DAbstract Authors: Soggiu A, Marullo O, Roncada P, Capobianco E Typical high-abundant proteins, including albumin, IgG, IgA and others, are the target of depletion methods usually applied to two-dimensional electrophoresis (2DE) of human biological fluids like serum and plasma. Detection of low-abundant proteins is of interest with regard to biomarkers for disease when being studied by 2DE or liquid chromatography-mass spectrometry (LC/MS). After depletion of very abundant proteins, serum samples consist of an enriched pool of low-abundant proteins that can be further studied without significant interferences, thus allowing for a full identification of the low abundant proteins, whose spots become now more visible. We have employed wavelet-based techniques and their derived denoisers to explore ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858577 Sun, 04 Oct 2009 18:16:03 +0100 2858577 http://www.medworm.com/index.php?rid=2858576&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19795571%26dopt%3DAbstract In this study, Support Vector Machine (SVM) models have been developed for predicting poly(A) signals in a DNA sequence using 100 nucleotides, each upstream and downstream of this signal. Here, we introduced a novel split nucleotide frequency technique, and the models thus developed achieved maximum Matthews correlation coefficients (MCC) of 0.58, 0.69, 0.70 and 0.69 using mononucleotide, dinucleotide, trinucleotide, and tetranucleotide frequencies, respectively. Finally, a hybrid model developed using a combination of dinucleotide, 2nd order dinucleotide and tetranucleotide frequencies, achieved a maximum MCC of 0.72. Moreover, for independent datasets this model achieved a precision ranging from 75.8-95.7% with a sensitivity of 57%, which is better than any other known methods. PMID:... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2858576 Sun, 04 Oct 2009 18:16:03 +0100 2858576 http://www.medworm.com/index.php?rid=2547605&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537157%26dopt%3DAbstract Authors: Sau K, Deb A To see the effect of temperature on the codon and amino acid usage in phages, codon and amino acid usage of 13 phages of extremely thermophilic prokaryotes were compared with that of 14 phages of mesophilic prokaryotes. Correspondence analysis on RSCU values of two groups of phage genomes clearly shows that phages are separated along the second major axis according to their growth temperature, whereas, they are separated along the first major axis according to their GC content. Correspondence analysis on RAAU values of two groups of phages clearly shows that protein encoding genes of the phages along the second major axis are highly correlated with the GRAVY, aromaticity and cysteine content. Moreover, correspondence analysis on the regular and irregular structure... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547605 Sun, 28 Jun 2009 04:45:03 +0100 2547605 http://www.medworm.com/index.php?rid=2547604&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537158%26dopt%3DAbstract Authors: Ecker K, Lichtenberg J, Welch L In this paper we describe some utilizing conditions of a recently published tool that offers two basic functions for the classical problem of discovering motifs in a set of promoter sequences. For the first it is assumed that not necessarily all of the sequences possess a common motif of given length l. In this case, CHECKPROMOTER allows an exact identification of maximal subsets of related promoters. The purpose of this program is to recognize putatively co-regulated genes. The second, CHECKMOTIF, solves the problem of checking if the given promoters have a common motif. It uses a fast approximation algorithm for which we were able to derive non-trivial low performance bounds (defined as the ratio of Hamming distance of the obtained solution to... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547604 Sun, 28 Jun 2009 04:45:03 +0100 2547604 http://www.medworm.com/index.php?rid=2547603&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537159%26dopt%3DAbstract Authors: Kohonen J, Talikota S, Corander J, Auvinen P, Arjas E A Naive Bayes classifier tool is presented for annotating proteins on the basis of amino acid motifs, cellular localization and protein-protein interactions. Annotations take the form of posterior probabilities within the Molecular Function hierarchy of the Gene Ontology (GO). Experiments with the data available for yeast, Saccharomyces cerevisiae, show that our prediction method can yield a relatively high level of accuracy. Several apparent challenges and possibilities for future developments are also discussed. A common approach to functional characterization is to use sequence similarities at varying levels, by utilizing several existing databases and local alignment/identification algorithms. Such an approach is typica... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547603 Sun, 28 Jun 2009 04:45:03 +0100 2547603 http://www.medworm.com/index.php?rid=2547602&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537160%26dopt%3DAbstract Authors: Garg P, Sharma V, Chaudhari P, Roy N High-throughput genome sequencing projects continue to churn out enormous amounts of raw sequence data. However, most of this raw sequence data is unannotated and, hence, not very useful. Among the various approaches to decipher the function of a protein, one is to determine its localization. Experimental approaches for proteome annotation including determination of a protein's subcellular localizations are very costly and labor intensive. Besides the available experimental methods, in silico methods present alternative approaches to accomplish this task. Here, we present two machine learning approaches for prediction of the subcellular localization of a protein from the primary sequence information. Two machine learning algorithms, k Neare... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547602 Sun, 28 Jun 2009 04:45:03 +0100 2547602 http://www.medworm.com/index.php?rid=2547601&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537161%26dopt%3DAbstract Authors: Singh TR, Pardasani KR Restriction endonucleases represent one of the best studied examples of DNA binding proteins. Type II restriction endonucleases recognize short sequences of foreign DNA and cleave the target on both strands with remarkable sequence specificity. Type II restriction endonucleases are part of restriction modification systems. Restriction modification systems occur ubiquitously among bacteria and archaea. Restriction endonucleases are indispensable tools in molecular biology and biotechnology. They are important model system for specific protein-nucleic acid interactions and also serve as good example for investigating structural, functional and evolutionary relationships among various biomolecules. The interaction between restriction endonucleases and their... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547601 Sun, 28 Jun 2009 04:45:03 +0100 2547601 http://www.medworm.com/index.php?rid=2547600&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537162%26dopt%3DAbstract Authors: Rani TS, Bapi RS Promoter prediction is an important and complex problem. Pattern recognition algorithms typically require features that could capture this complexity. A special bias towards certain combinations of base pairs in the promoter sequences may be possible. In order to determine these biases n-grams are usually extracted and analyzed. An n-gram is a selection of n contiguous characters from a given character stream, DNA sequence segments in this case. Here a systematic study is made to discover the efficacy of n-grams for n = 2, 3, 4, 5 in promoter prediction. A study of n-grams as features for a neural network classifier for E. coli and Drosophila promoters is made. In case of E. coli n=3 and in case of Drosophila n=4 seem to give optimal prediction values. Using t... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547600 Sun, 28 Jun 2009 04:45:03 +0100 2547600 http://www.medworm.com/index.php?rid=2547599&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537163%26dopt%3DAbstract This study therefore illustrates the power of using relevant biological information, in the form of a set of differentially expressed genes that is a classical outcome in most of transcriptomics studies. This allows to severely reduce the search space and to design an adapted statistical indicator. Taken together, this allows the biologist to concentrate on a small number of putatively interesting TFs. PMID: 19537163 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547599 Sun, 28 Jun 2009 04:45:03 +0100 2547599 http://www.medworm.com/index.php?rid=2547598&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537164%26dopt%3DAbstract Authors: Roy A, Srinivasan N, Gowri VS Using a large database of protein domain families of known 3-D structure we present an analysis on the relationships among sequences, structures and functions of closely-related enzymes performed at the level of catalytic domains. Only in 38% of the pairs of homologous catalytic domains characterized by over about 60% of sequence identity the functions are almost completely identical. Nearly 43% of the pairs differ in their substrate specificity. Hence the most common variation of enzyme function among the closely-related homologues is the differences in the substrate specificity. For homologous pairs characterized by a sequence identity of 30-60%, if the structural difference metric is less than about 30, the functions are highly conserved. For c... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547598 Sun, 28 Jun 2009 04:45:03 +0100 2547598 http://www.medworm.com/index.php?rid=2547597&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19537165%26dopt%3DAbstract Authors: Ganesh AB, Rajasingh H, Mande SS Salmonella enterica serovar Typhimurium invades the intestinal epithelial cells using type three secretion system (TTSS) encoded on Salmonella pathogenicity island-1 (SPI-1). The key regulator of this secretion system is HilA, which is in turn regulated by HilD, HilC and RtsA. It is also known that SirA/BarA system, a two-component regulatory system plays a crucial role in regulating HilA. There are two different mechanisms that have been proposed earlier for regulation of HilD-HilC-RtsA-HilA network by SirA. One considers SirA to be acting through HilA and HilC, whereas the other considers SirA to be acting through HilD. In this paper, we have built mathematical models corresponding to both these scenarios and carried out simulations under dif... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2547597 Sun, 28 Jun 2009 04:45:03 +0100 2547597 http://www.medworm.com/index.php?rid=2020927&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032156%26dopt%3DAbstract In this study, we have done sequence analysis, homology modeling and docking studies of a typical member of the P25 family of ookinete surface protein, i.e. Pfs25 from Plasmodium falciparum. We have built a 3D model of Pfs25 based on the X-ray crystallographic structure of Pvs25 from Plasmodium vivax. Also we have modeled the Fv region of the malaria transmission blocking monoclonal antibody 4B7. This antibody is the transmission blocking monoclonal antibody for Pfs25 protein. Pfs25 and 4B7 scFv (single chain variable fragment only) docking results indicate that EGF domain III of the Pfs25 protein interacts with the scFv region of modeled 4B7 antibody forming seven hydrogen bonds out of which six are formed with heavy chain of scFv region. Docking results of Pfs25 with gamma chain of lamin... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=2020927 Tue, 09 Dec 2008 05:07:27 +0100 2020927 http://www.medworm.com/index.php?rid=1995090&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032156%26dopt%3DAbstract In this study, we have done sequence analysis, homology modeling and docking studies of a typical member of the P25 family of ookinete surface protein, i.e. Pfs25 from Plasmodium falciparum. We have built a 3D model of Pfs25 based on the X-ray crystallographic structure of Pvs25 from Plasmodium vivax. Also we have modeled the Fv region of the malaria transmission blocking monoclonal antibody 4B7. This antibody is the transmission blocking monoclonal antibody for Pfs25 protein. Pfs25 and 4B7 scFv (single chain variable fragment only) docking results indicate that EGF domain III of the Pfs25 protein interacts with the scFv region of modeled 4B7 antibody forming seven hydrogen bonds out of which six are formed with heavy chain of scFv region. Docking results of Pfs25 with gamma chain of lamin... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995090 Sat, 29 Nov 2008 04:57:04 +0100 1995090 http://www.medworm.com/index.php?rid=1995089&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032157%26dopt%3DAbstract Authors: Vinod PK, Venkatesh KV Occurrence of multiple upstream activation sites (UASs) is a structural motif that is observed within the promoter of eukaryotic genes for coordinating gene expression. Transcriptional activation depends on the ability of transcriptional activators to bind to its specific UASs, which are kept inaccessible due to the nucleosomal organization of the chromatin. Targeting of chromatin remodeling complexes by a sequence specific transcriptional activator is shown to be detrimental for transcriptional initiation. Here, we analyze such a regulatory structure involving ordered recruitment of transcriptional activators and chromatin remodeling complexes with respect to activation of a flocculin gene, FLO11 involved in the filamentous growth to gain insights into ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995089 Sat, 29 Nov 2008 04:57:04 +0100 1995089 http://www.medworm.com/index.php?rid=1995088&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032158%26dopt%3DAbstract Authors: Pundhir S, Vijayvargiya H, Kumar A Pathogenicity Islands (PAIs) are the sub-sets of Genomic Islands (GIs) that are acquired by horizontal gene transfer (HGT) and are generally shown to have a significant deviation in G+C, dinucleotide or codon frequency from core genome. Major approaches used for PAI identification are based on composition bias and/or similarity with known PAIs. These approaches either limit the search to GIs or to regions similar to previously annotated PAIs. PredictBias is a web application for the identification of genomic and pathogenicity islands in prokaryotes based on composition bias, presence of insertion elements, proximity with virulence-associated genes and absence in related non-pathogenic species. A profile database of virulence factors (VFPD) ha... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995088 Sat, 29 Nov 2008 04:57:04 +0100 1995088 http://www.medworm.com/index.php?rid=1995087&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032159%26dopt%3DAbstract We present a simple and generally applicable bioinformatics approach for the analysis of possible interactions between the proteins of a parasite, Plasmodium falciparum, and human host. In the first step, the physically compatible interactions between the parasite and human proteins are recognized using homology detection. This dataset of putative in vitro interactions is combined with large-scale datasets of expression and sub-cellular localization. This integrated approach reduces drastically the number of false positives and hence can be used for generating testable hypotheses. We could recognize known interactions previously suggested in the literature. We also propose new predictions which involve interactions of some of the parasite proteins of yet unknown function. The method descri... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995087 Sat, 29 Nov 2008 04:57:04 +0100 1995087 http://www.medworm.com/index.php?rid=1995086&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032160%26dopt%3DAbstract Authors: Ram S, Singh RL, Shanker R Rapid diagnostics and risk assessment of the pathogens is possible by Real-Time Polymerase Chain Reaction (PCR) probes like TaqMan, Molecular Beacon (MB) and FRET. However, validation of such probes for real-life samples is an expensive and time consuming proposition. Hence, development and comparison of real-time probes in silico can be the first step in selection of most appropriate probe chemistry. The virulence genes specific for a model pathogen, Escherichia coli O157:H7, transmitted worldwide by contaminated water and food, were chosen to compare probe chemistries. MB was observed to be the best probe chemistry for virulence genes stx1, stx2 and eae, while FRET was preferred for hlyA gene, based on Tm and free energy values for self-dimer, hair... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995086 Sat, 29 Nov 2008 04:57:04 +0100 1995086 http://www.medworm.com/index.php?rid=1995085&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032161%26dopt%3DAbstract Authors: Anand S, Anbarasu A, Sethumadhavan R We have explored the roles played by C-H...pi hydrogen bonds in interleukins. Main-chain to side-chain C-H...pi interactions are the predominant type of interactions in interleukins. There was an average of 15 C-H...pi interactions per protein and also there was an average of one significant C-H...pi interaction for every 14 residues in the interleukins investigated. Significant contribution to C-H...pi interactions was only from Asp, Gly, His, Lys, Phe, Pro, Ser, Thr, Trp and Tyr in interleukins. Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain 5 member aromatic ring and side-chain to side-chain C-H...pi interactions. Short and medium-range C-H...pi interactions are the predominant type of... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995085 Sat, 29 Nov 2008 04:57:04 +0100 1995085 http://www.medworm.com/index.php?rid=1995084&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032162%26dopt%3DAbstract Authors: Sengupta D, Verma D, Naik PK Nevirapine and its synthetic analogues, a class of non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT), have been the objective of numerous studies focused to prepare better and safer anti-HIV drugs. We developed a library of nevirapine analogues (47) using combinatorial design and with structural modification at X, Y and R substituents in the parent structure of nevirapine. Their molecular interactions and binding affinities with reverse transcriptase (3HVT and 1VRT) have been studied using the docking-molecular mechanics based generalized Born/surface area (MM-GB/SA) solvation model. Final screening of these analogues is based on absorption, distribution, metabolism and excretion (ADME) properties. The proposed NNRTI analogues ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995084 Sat, 29 Nov 2008 04:57:04 +0100 1995084 http://www.medworm.com/index.php?rid=1995083&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032163%26dopt%3DAbstract Authors: Wen J, Frickey T, Weiller GF Identification and analysis of miRNAs enhances our understanding of the important roles that small RNAs play in complex regulatory networks. It is often difficult to perform large-scale validation of miRNA expression that is predicted from genomic regions. Expressed transcripts provide an alternative resource to facilitate identification of miRNAs and their targets. We developed a computational pipeline to scan for miRNA genes from polyadenylated transcripts that were associated with limited protein coding potentials, corresponding to the intergenic regions of Medicago truncatula genomic sequences. Each predicted miRNA was required to have a near perfect match with target genes. We also searched for miRNA conservation in other plant species, cluste... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995083 Sat, 29 Nov 2008 04:57:04 +0100 1995083 http://www.medworm.com/index.php?rid=1995082&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032164%26dopt%3DAbstract Authors: Kanagarajadurai K, Sowdhamini R Interleukin-8 and related chemokines are small proteins that bind to receptors belonging to the large family of G-protein-coupled receptors. They can cause migration of cells like neutrophils and eosinophils and some of them are implicated in angiogenic diseases. More than 40 subfamilies of these ligands are known that share poor sequence similarity and display receptor specificity. There is very little structural information about the mode of binding between ligands and the receptors. We have employed multi-fold sensitive sequence search methods to provide a repertoire of 252 putative interleukin-8 proteins and homologues, which are shared across humans, aves and fish. The sequences can be organized into five major known clusters. The propensit... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995082 Sat, 29 Nov 2008 04:57:04 +0100 1995082 http://www.medworm.com/index.php?rid=1995081&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032165%26dopt%3DAbstract Authors: Sharma V, Gupta P, Dixit A Aeromonas hydrophila is a major pathogen both of aquatic and terrestrial organisms, including humans. Infection with A. hydrophila results in severe economic losses to the aquaculture industry. In humans, Aeromonas hydrophila infections are known to cause gastroenteritis and wound infections. Investigations for developing a potential vaccine for its control are underway. The availability of the complete sequence information of A. hydrophila strain ATCC 7966T genome has made it possible to carry out the in silico analysis of its genome for various aspects of its biology. Keeping in view the possible risks that A. hydrophila poses to humans, in silico analysis of the A. hydrophila genome was carried out for the identification of potential vaccine and d... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995081 Sat, 29 Nov 2008 04:57:04 +0100 1995081 http://www.medworm.com/index.php?rid=1995080&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032166%26dopt%3DAbstract Authors: Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a Web site that has been designed and implemented to support research and analysis workflows ranging from metabolome to transcriptome analysis. The site provides access to a growing collection of standardized measurements of metabolites obtained by using NMR, GC-MS, LC-MS, and CE-MS, and metabolomics tools that support related analyses (SpinAssign for the identification of metabolites by means of NMR, KNApSAcK for searches within metabolite databases). In addition, the transcriptomics tools provide Correlated Gene Search, and Cluster Cutting for the analysis of mRNA expression. Use of the tools and... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995080 Sat, 29 Nov 2008 04:57:04 +0100 1995080 http://www.medworm.com/index.php?rid=1995079&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032167%26dopt%3DAbstract Authors: Kamasawa M, Horiuchi J A large-scale analysis of human polyadenylation signals was carried out in silico. The most canonical AAUAAA hexamer and its 11 single-nucleotide variants that are most frequent in human genes were used to search for polyadenylation signals in the terminal sequences. Out of 18,277 poly(A) sites that were identified from 26,414 human genes, 82.5% of the sites were found to contain at least one of these 12 hexamers as a polyadenylation signal within 40 nucleotides upstream of the poly(A) site. The rest (17.5%) did not contain any of these hexamers, which suggests the existence of yet unknown signals. A total of 20,347 terminal sequences in close proximity to 12 polyadenylation signals were collected using modified EST clustering technique to establish a la... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995079 Sat, 29 Nov 2008 04:57:04 +0100 1995079 http://www.medworm.com/index.php?rid=1995078&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19032168%26dopt%3DAbstract Authors: Khalid S, Khan M, Gorle CB, Fraser K, Wang P, Liu X, Li S Microarray gene expression datasets are continually being placed in public repositories. As a result, one of the most important emerging challenges is that which enables researchers to take full advantage of such previously accumulated data to discover or validate common genes in similar biological systems. In light of this we have designed the MaXlab software to not only cross-compare available array data from different laboratories but also extract further knowledge from gene expression patterns embedded within published data. More importantly MaXlab offers a flexible and automated solution applicable for microarray technologies including cDNA and Affymetrix gene chips generating expression profiles for common genes w... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1995078 Sat, 29 Nov 2008 04:57:04 +0100 1995078 http://www.medworm.com/index.php?rid=1899728&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928197%26dopt%3DAbstract Authors: Yan Q Viruses are major factors of human infectious diseases. Understanding of the structure-function correlation in viruses is important for the identification of potential anti-viral inhibitors and vaccine targets. In virology research, virus-related databases and bioinformatic analysis tools are essential for discerning relationships within complex datasets about viruses and host-virus interactions. Bioinformatic analyses on viruses include the identification of open reading frames, gene prediction, homology searching, sequence alignment, and motif and epitope recognition. The predictions of features such as transmembrane domains, glycosylation sites, and protein secondary and tertiary structure are important for analyzing the structure-function relationship of proteins enc... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899728 Fri, 24 Oct 2008 08:49:56 +0100 1899728 http://www.medworm.com/index.php?rid=1899727&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928198%26dopt%3DAbstract Authors: Rajendrakumar P, Biswal AK, Balachandran SM, Sundaram RM Microsatellites are abundant across prokaryotic and eukaryotic genomes. However, comparative analysis of microsatellites in the organellar genomes of plants and their utility in understanding phylogeny has not been reported. The purpose of this study was to understand the organization of microsatellites in the coding and non-coding regions of organellar genomes of major cereals viz., rice, wheat, maize and sorghum. About 5.8-14.3% of mitochondrial and 30.5-43.2% of chloroplast microsatellites were observed in the coding regions. About 83.8-86.8% of known mitochondrial genes had at least one microsatellite while this value ranged from 78.6-82.9% among the chloroplast genomes. Dinucleotide repeats were the most abundant in... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899727 Fri, 24 Oct 2008 08:49:56 +0100 1899727 http://www.medworm.com/index.php?rid=1899726&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928199%26dopt%3DAbstract Authors: Cohen A, Bocobza S, Veksler I, Gabdank I, Barash D, Aharoni A, Shapira M, Kedem K Three-way junctions in folded RNAs have been investigated both experimentally and computationally. The interest in their analysis stems from the fact that they have significantly been found to possess a functional role. In recent work, three-way junctions have been categorized into families depending on the relative lengths of the segments linking the three helices. Here, based on ideas originating from computational geometry, an algorithm is proposed for detecting three-way junctions in data sets of genes that are related to a metabolic pathway of interest. In its current implementation, the algorithm relies on a moving window that performs energy minimization folding predictions, and is demonst... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899726 Fri, 24 Oct 2008 08:49:56 +0100 1899726 http://www.medworm.com/index.php?rid=1899725&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928200%26dopt%3DAbstract Authors: Kumar M, Thakur V, Raghava GP In the past, a large number of methods have been developed for predicting various characteristics of a protein from its composition. In order to exploit the full potential of protein composition, we developed the web-server COPid to assist the researchers in annotating the function of a protein from its composition using whole or part of the protein. COPid has three modules called search, composition and analysis. The search module allows searching of protein sequences in six different databases. Search results list database proteins in ascending order of Euclidian distance or descending order of compositional similarity with the query sequence. The composition module allows calculation of the composition of a sequence and average composition of a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899725 Fri, 24 Oct 2008 08:49:56 +0100 1899725 http://www.medworm.com/index.php?rid=1899724&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928201%26dopt%3DAbstract In this study, a systematic attempt has been made to predict secretory proteins irrespective of presence or absence of N-terminal signal peptides (also known as classical and non-classical secreted proteins respectively), using machine-learning techniques; artificial neural network (ANN) and support vector machine (SVM). We trained and tested our methods on a dataset of 3321 secretory and 3654 non-secretory mammalian proteins using five-fold cross-validation technique. First, ANN-based modules have been developed for predicting secretory proteins using 33 physico-chemical properties, amino acid composition and dipeptide composition and achieved accuracies of 73.1%, 76.1% and 77.1%, respectively. Similarly, SVM-based modules using 33 physico-chemical properties, amino acid, and dipeptide co... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899724 Fri, 24 Oct 2008 08:49:56 +0100 1899724 http://www.medworm.com/index.php?rid=1899723&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928202%26dopt%3DAbstract We present here a robust computational method for finding new G proteins and their homologs using a SVM based pattern recognition algorithm. Several physicochemical and compositional properties including dipeptide, tripeptide and hydrophobicity composition are used for generating the SVM classifiers. This method has 96.17%, 95.38%, 97.6% sensitivity and 99.45%, 100%, 100% specificity on test sets for G protein alpha, beta, and gamma subunits, respectively. This algorithm correctly predicts the known alpha, beta and gamma subunits reported in literature. One important contribution of this algorithm is that it helps in improving genome annotation of several proteins as G proteins and serves as a useful tool for comparative genomic analysis of G proteins. Using this method, novel G protein su... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899723 Fri, 24 Oct 2008 08:49:56 +0100 1899723 http://www.medworm.com/index.php?rid=1899722&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928203%26dopt%3DAbstract Authors: Klémal J, Blachon S, Soulet A, Crémilleux B, Gandrillon O Current analyses of co-expressed genes are often based on global approaches such as clustering or bi-clustering. An alternative way is to employ local methods and search for patterns--sets of genes displaying specific expression properties in a set of situations. The main bottleneck of this type of analysis is twofold--computational costs and an overwhelming number of candidate patterns which can hardly be further exploited. A timely application of background knowledge available in literature databases, biological ontologies and other sources can help to focus on the most plausible patterns only. The paper proposes, implements and tests a flexible constraint-based framework that enables the effective mining an... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899722 Fri, 24 Oct 2008 08:49:56 +0100 1899722 http://www.medworm.com/index.php?rid=1899721&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928204%26dopt%3DAbstract Authors: Pommerenke C, Gabriel I, Bunk B, Münch R, Haddad I, Tielen P, Wagner-Döbler I, Jahn D Systems biology approaches to bacteria require an integrated database and a bioinformatics tool platform to enable automated and manual annotation, regulatory and metabolic network deduction, and the storage of related experimental as well as predicted data. In this context ROSY--the Roseobacter SYstems biology database--was developed for completed and draft genomes of representatives of the marine Roseobacter clade, which constitutes one of the most abundant bacterial clades in the ocean. ROSY provides an integrative view on comprehensive data collections such as KEGG, GenBank, RoseoBase, BRENDA, and PRODORIC as well as mediates the use of connected tools for promoter analysis (Vir... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899721 Fri, 24 Oct 2008 08:49:56 +0100 1899721 http://www.medworm.com/index.php?rid=1899720&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18928205%26dopt%3DAbstract Authors: Sandhu KS, Pandey S, Maiti S, Pillai B Codon optimization is a generic technique to achieve optimum expression of a foreign gene in the host's cell system. Selection of optimum codons depends on codon usage of the host genome and the presence of several desirable and undesirable sequence motifs. Searching these motifs in all possible combinations of the codons increases the search space exponentially with respect to sequence length. GASCO is an algorithm developed for the optimum codon selection using genetic algorithms. The algorithm reduces the search space and provides an approximate solution to the problem. The algorithm has applications in DNA vaccine design for successfully eliciting potent immune responses and synthetic gene design for metabolic pathway engineering. The... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1899720 Fri, 24 Oct 2008 08:49:56 +0100 1899720 http://www.medworm.com/index.php?rid=1395867&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430985%26dopt%3DAbstract Authors: Bumpus JA, Trax M, Reisdorph A, Boyd C, Gilbert D, Techau S, Ventullo RM An in silico approach was used to investigate cytochrome c and the cytochrome c gene of Phanerochaete chrysosporium. The cytochrome c gene contains four introns. Omission of the introns reveals a DNA sequence coding for a complete predicted amino acid sequence for P. chrysosporium cytochrome c consistent with those of other cytochromes c. Fungal cytochromes c often have a short N-terminal peptide preceding a Gly that is the N-terminal amino acid in many cytochromes c. Thus a microexon codes for an N-terminal pentapeptide (MetProTyrAlaPro) in P. chrysosporium that is identical to the N-terminal pentapeptide of Schizosaccharomyces pombe, a well studied yeast, the genome of which bears more similarity to hig... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395867 Thu, 24 Apr 2008 19:35:55 +0100 1395867 http://www.medworm.com/index.php?rid=1395866&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430986%26dopt%3DAbstract Authors: Arenas AF, Escobar AJ, Gómez-Marin JE The histone-like proteins (HU) belong to a family of DNA architectural proteins that stabilize nucleoprotein complexes. We found a putative HU protein (TgGlmHMM_3045) in Toxoplasma gondii genome that was homologous to the bacterial HU protein. This putative sequence was located in the scaffold TGG_995361 of the chromosome 10. The sequence included the prokaryotic bacterial histone-like domain, KFGSLGlRRRGERVARNPRT (ID number PS00045). HU protein sequences were also found in Plasmodium falciparum, Neospora caninum, Theileria parva and Theileria annulata. We found that the homology of the putative HU protein in Apicomplexa was greater with bacterial histone-like proteins than with eukaryotic histone proteins. The phylogenetic tree indic... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395866 Thu, 24 Apr 2008 19:35:55 +0100 1395866 http://www.medworm.com/index.php?rid=1395865&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430987%26dopt%3DAbstract Authors: Xu Z, Chao Y, Si Y, Wang J, Jin M, Guo A, Qian P, Zhou R, Chen H The NS5B protein of classical swine fever virus (CSFV) is an important enzyme bearing a unique RNA-dependent RNA polymerase (RdRp) activity. The RdRp plays a crucial role in the viral replication cycle and in forming a replicase complex. However, the initiating synthesis mechanism of the CSFV RNA polymerase is unclearly described at present. Our aim is to reveal the RdRp-GTP docking sites and the effective modules of GTP initially bound to the polymerase in starting initiation of replication according to a well predicted CSFV RdRp model. Based on some known crystal structures of RNA polymerase, computational methods were used to establish the model of a CSFV RdRp. An analogous mechanism of CSFV RNA polymerase in ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395865 Thu, 24 Apr 2008 19:35:55 +0100 1395865 http://www.medworm.com/index.php?rid=1395864&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430988%26dopt%3DAbstract Authors: Furney SJ, Madden SF, Kisiel TA, Higgins DG, Lopez-Bigas N Understanding the mechanism of regulation of cancer genes and the constraints on their coding sequences is of fundamental importance in understanding the process of tumour development. Here we test the hypothesis that tumour suppressor genes and proto-oncogenes, due to their involvement in tumourigenesis, have distinct patterns of regulation and coding selective constraints compared to non-cancer genes. Indeed, we found significantly greater conservation in the promoter regions of proto-oncogenes, suggesting that these genes are more tightly regulated, i.e. they are more likely to contain a higher density of cis-regulatory elements. Furthermore, proto-oncogenes appear to be preferentially targeted by microRNAs and have... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395864 Thu, 24 Apr 2008 19:35:55 +0100 1395864 http://www.medworm.com/index.php?rid=1395863&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430989%26dopt%3DAbstract Authors: Yang L, Walker JR, Hogenesch JB, Thomas RS Graphical methods are useful for visualizing signaling networks derived from the synthesis of large bodies of literature information or large-scale experimental measurements. Software tools to filter and organize these networks allow the exploration of their inherent biological and structural properties. We have developed NetAtlas, an open-source, Java-based Cytoscape plugin for examining signaling networks in the context of tissue gene expression patterns. The tissue gene expression data available through NetAtlas consists of 79 human tissues, 61 mouse tissues, and 44 combined tissues from 3 rat strains. Users may also import their own tissue gene expression data. The NetAtlas plugin allows the creation of tissue-defined signaling ne... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395863 Thu, 24 Apr 2008 19:35:55 +0100 1395863 http://www.medworm.com/index.php?rid=1395862&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430990%26dopt%3DAbstract Authors: Nakazato T, Takinaka T, Mizuguchi H, Matsuda H, Bono H, Asogawa M Microarray technology has become employed widely for biological researchers to identify genes associated with conditions such as diseases and drugs. To date, many methods have been developed to analyze data covering a large number of genes, but they focus only on statistical significance and cannot decipher the data with biological concepts. Gene Ontology (GO) is utilized to understand the data with biological interpretation; however, it is restricted to specific ontology such as biological process, molecular function, and cellular component. Here, we attempted to apply MeSH (Medical Subject Headings) to interpret groups of genes from biological viewpoint. To assign MeSH terms to genes, in this study, contexts a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395862 Thu, 24 Apr 2008 19:35:55 +0100 1395862 http://www.medworm.com/index.php?rid=1395861&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18430991%26dopt%3DAbstract Authors: Le Béchec A, Zindy P, Sierocinski T, Petritis D, Bihouée A, Le Meur N, Léger J, Théret N Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningful gene interaction networks, integrated software solutions are still needed. Therefore, we developed M@IA, an environment for DNA microarray data analysis allowing gene network reconstruction. M@IA is a microarray integrated application which includes all of the steps of a microarray study, from MIAME-compliant raw data storag... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=1395861 Thu, 24 Apr 2008 19:35:55 +0100 1395861 http://www.medworm.com/index.php?rid=963738&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822385%26dopt%3DAbstract Authors: PMID: 17822385 [PubMed - indexed for MEDLINE] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=963738 Fri, 19 Oct 2007 23:58:16 +0100 963738 http://www.medworm.com/index.php?rid=871390&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822385%26dopt%3DAbstract Authors: Rojas I, Wittig U PMID: 17822385 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871390 Sat, 15 Sep 2007 00:18:16 +0100 871390 http://www.medworm.com/index.php?rid=871389&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822386%26dopt%3DAbstract Authors: Wingender E, Hogan J, Schacherer F, Potapov AP, Kel-Margoulis O The HumanPSD database on the complete proteomes of human, mouse and rat has been integrated with the databases TRANSFAC on gene regulation and TRANSPATH on signal transduction to provide a comprehensive systems biological platform for these organisms. As a next step, integration with PathoDB and PathoSign on pathologically relevant mutations is planned together with an extension beyond the limits of the individual cell, towards intercellular networks, by integrating the database EndoNet on hormonal networks as well. The overall aim is to come up with a platform that is suitable to provide knowledge for systems pathology, i. e. a system-wide modeling of pathological states and their development. PMID: 17822386 ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871389 Sat, 15 Sep 2007 00:18:16 +0100 871389 http://www.medworm.com/index.php?rid=871388&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822387%26dopt%3DAbstract Authors: van Gend C, Conradie R, du Preez FB, Snoep JL Systems Biology requires a tight integration of experimental data and detailed computer models to obtain a quantitative understanding of the system under study. To facilitate this integration a standardization of data and model representation and storage is important. We illustrate here such an integration using JWS Online, the modeling tool developed in our group. We follow the approach of the Silicon Cell project for the construction and validation of kinetic models and discuss some issues with respect to storage of experimental data and models. The majority of the published kinetic models for biological systems have been developed for metabolic networks and this will be our focus in this manuscript. It is not our aim to present ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871388 Sat, 15 Sep 2007 00:18:16 +0100 871388 http://www.medworm.com/index.php?rid=871387&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822388%26dopt%3DAbstract Authors: Cánovas M, Bernal V, Sevilla A, Iborra JL A thorough understanding of the in vivo kinetics of microorganisms requires the analysis of different data sets and therefore needs support from different sources of genome, transcriptome, proteome and metabolome data, as well as to generate new data in the laboratory to depict cell phenotypes in different scenarios. The value of dynamic metabolic data depends on the adequate design of wet experiments. In this paper a schematic representation of wet dynamic experiments to generate data is discussed. As a case study, the linking of the central metabolism with the carnitine secondary metabolism in E. coli is presented. The feed-back between the data generated and in silico modeling helps our understanding of the Escherichia coli exp... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871387 Sat, 15 Sep 2007 00:18:16 +0100 871387 http://www.medworm.com/index.php?rid=871386&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822389%26dopt%3DAbstract Authors: Rojas I, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Wittig U This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such annotations support the definition of cross links to other related databases and augment the semantics of the data stored in the database. PMID: 17822389 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871386 Sat, 15 Sep 2007 00:18:16 +0100 871386 http://www.medworm.com/index.php?rid=871385&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822390%26dopt%3DAbstract We present some challenges and achievements in the standardisation of chemical language in biological databases, with emphasis on three aspects of annotation: 1. good drawing practice: how to draw unambiguous 2-D diagrams; 2. good naming practice: how to give most appropriate names; and 3. good ontology practice: how to link the entity of interest by defined logical relationships to other entities. PMID: 17822390 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871385 Sat, 15 Sep 2007 00:18:16 +0100 871385 http://www.medworm.com/index.php?rid=871384&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822391%26dopt%3DAbstract Authors: Kettner C Systems level investigation of genomic and proteomic scale information requires incomparably higher demands for data quality than in previous decades. Truly integrated databases that deal with heterogeneous data need to be developed to be able to retrieve properties of genes, for kinetics of enzymes, for behaviour of complex networks and for the analysis and modelling of complex biological processes. Despite the fast paced global efforts in biological systems research, the current analyses are limited by the lack of available systematic collections of comparable functional enzyme data. Besides its reliability, these data have to provide defined minimum experimental information, they must be available from the literature along with their accepted enzyme names, and mus... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871384 Sat, 15 Sep 2007 00:18:16 +0100 871384 http://www.medworm.com/index.php?rid=871383&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822392%26dopt%3DAbstract Authors: Kummer U Computational approaches to biochemistry like modeling and simulation are dependent on the availability of kinetic information. This information can either be directly derived from experimental data generated by collaborators or has to be digged up from literature, often both. More recently, data stored in databases has started to be a valuable addition as a source of enzyme kinetic data. In order to faciliate modeling and simulation, various tools have been developed in recent years. However, automatizing steps in setting up, analyzing or simulating models requires the data to be in defined formats. Crucial points are addressed below. PMID: 17822392 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871383 Sat, 15 Sep 2007 00:18:16 +0100 871383 http://www.medworm.com/index.php?rid=871382&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822393%26dopt%3DAbstract We describe a workflow to translate a given metabolic network into a kinetic model; the model summarises kinetic information collected from different data sources. All reactions are modelled by convenience kinetics; where detailed kinetic laws are known, they can also be incorporated. Confidence intervals and correlations of the resulting model parameters are obtained from Bayesian parameter estimation; they can be used to sample parameter sets for Monte-Carlo simulations. The integration method ensures that the resulting parameter distributions are thermodynamically feasible. Here we summarise different previous works on this topic: we give an overview over the convenience kinetics, thermodynamic criteria for parameter sets, Bayesian parameter estimation, the collection of kinetic data, a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871382 Sat, 15 Sep 2007 00:18:16 +0100 871382 http://www.medworm.com/index.php?rid=871381&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17822394%26dopt%3DAbstract Authors: Funahashi A, Jouraku A, Matsuoka Y, Kitano H Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge for systems biology. To facilitate this research topic, we have developed CellDesigner to visualize, model and simulate biochemical networks. CellDesigner allows the users to easily create networks using solidly defined and comprehensive graphical notation. CellDesigner utilizes SBML to described models and can simulate models using an integrated SBML ODE Solver or third party simulation engine; thus enabling users to simulate through a sophisticated graphical user interface. Although CellDesigner can integrate with existing databases (KEGG, PubMed, BioModels, etc.), by calling a web browser, or connecting to its web page through HT... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=871381 Sat, 15 Sep 2007 00:18:16 +0100 871381 http://www.medworm.com/index.php?rid=807140&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688431%26dopt%3DAbstract Authors: Saha D, Prasad AM, Sujatha TP, Kumar V, Jain PK, Bhat SR, Srinivasan R A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene LOJ in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the LOJ gene. Out of numerous cis-elements detected in the LOJ promoter a few are considered important based on the expression pattern of the LOJ gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of a few genes involved in lateral organ development a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=807140 Sun, 19 Aug 2007 12:13:48 +0100 807140 http://www.medworm.com/index.php?rid=794783&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688426%26dopt%3DAbstract Authors: Tuncay K, Ensman L, Sun J, Haidar AA, Stanley F, Trelinski M, Ortoleva P Transcriptional regulatory network (TRN) discovery using information from a single source does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. A methodology, TRND, that integrates a preliminary TRN, gene expression data and gene ontology is developed to discover TRNs. The method is applied to a comprehensive set of expression data on B cell and a preliminary TRN that included 1,335 genes, 443 transcription factors (TFs) and 4032 gene/TF interactions. Predictions were obtained for 443 TFs and 9,589 genes. 14,616 of 4,247,927 possible gene/TF interactions scored higher than the imposed threshold. Results for three TFs, E2F-4, p130 and c-... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794783 Mon, 13 Aug 2007 12:40:25 +0100 794783 http://www.medworm.com/index.php?rid=794782&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688427%26dopt%3DAbstract We describe the implementation of some initial modules of the framework and apply them to a biological test case in bacterial regulation, which shows the relevance and feasibility of the proposed approach. PMID: 17688427 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794782 Mon, 13 Aug 2007 12:40:25 +0100 794782 http://www.medworm.com/index.php?rid=794781&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688428%26dopt%3DAbstract Authors: Yang Y, Tantoso E, Chua GH, Yeo ZX, Ng FS, Wong ST, Chung CW, Li KB P53 is probably the most important tumor suppressor known. Over the years, information about this gene has increased dramatically. We have built a comprehensive knowledgebase of p53, which aims to facilitate wet-lab biologists to formulate their experiments and new-comers to learn whatever they need about the gene and bioinformaticians to make new discoveries through data analysis. Using the information curated, including mutation information, transcription factors, transcriptional targets, and single nucleotide polymorphisms, we have performed extensive bioinformatics analysis, and made several new discoveries about p53. We have identified point missense mutations that are over-represented in cancers, but lac... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794781 Mon, 13 Aug 2007 12:40:25 +0100 794781 http://www.medworm.com/index.php?rid=794780&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688429%26dopt%3DAbstract Authors: Chopra P, Bender A We demonstrate the first application of cellular automata to the secondary structure predictions of proteins. Cellular automata use localized interactions to simulate global phenomena, which resembles the protein folding problem where individual residues interact locally to define the global protein conformation. The protein's amino acid sequence was input into the cellular automaton and rules for updating states were evolved using a genetic algorithm. An optimized accuracy (Q3) for the RS126 and CB513 dataset of 58.21% and 56.51%, respectively, could be obtained. Thus, the current work demonstrates the applicability of a rather simple algorithm on a problem as complex as protein secondary structure prediction. PMID: 17688429 [PubMed - in process] (Sourc... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794780 Mon, 13 Aug 2007 12:40:25 +0100 794780 http://www.medworm.com/index.php?rid=794779&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688430%26dopt%3DAbstract Authors: Paramasivan R, Sivaperumal R, Dhananjeyan KJ, Thenmozhi V, Tyagi BK Olfaction of insects is currently recognized as the major area of research for developing novel control strategies to prevent mosquito-borne infections. A 3-dimensional model (3D) was developed for the salivary gland odorant-binding protein-2 of the mosquito Culex quinquefasciatus, a major vector of human lymphatic filariasis. A homology modeling method was used for the prediction of the structure. For the modeling, two template proteins were obtained by mGenTHERADER, namely the high-resolution X-ray crystallography structure of a pheromone-binding protein (ASP1) of Apis mellifera L., [1R5R:A] and the aristolochene synthase from Penicillium roqueforti [1DI1:B]. By comparing the template protein a rough model w... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794779 Mon, 13 Aug 2007 12:40:25 +0100 794779 http://www.medworm.com/index.php?rid=794778&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688431%26dopt%3DAbstract Authors: Saha D, Prasad AM, Sujatha TP, Kumar V, Jain PK, Bhat SR, Srinivasan R A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene loj in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the loj gene. Out of numerous cis-elements detected in the loj promoter a few are considered important based on the expression pattern of the loj gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of a few genes involved in lateral organ development a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794778 Mon, 13 Aug 2007 12:40:25 +0100 794778 http://www.medworm.com/index.php?rid=794777&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688432%26dopt%3DAbstract Authors: Kong W, Tan TS, Tham L, Choo KW The identification and validation of protein allergens have become more important nowadays as more and more transgenic proteins are introduced into our food chains. Current allergen prediction algorithms focus on the identification of single motif or single allergen peptide for allergen detection. However, an analysis of the 575 allergen dataset shows that most allergens contain multiple motifs. Here, we present a novel algorithm that detects allergen by making use of combinations of motifs. Sensitivity of 0.772 and specificity of 0.904 were achieved by the proposed algorithm to predict allergen. The specificity of the proposed approach is found to be significantly higher than traditional single motif approaches. The high specificity of the prop... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794777 Mon, 13 Aug 2007 12:40:25 +0100 794777 http://www.medworm.com/index.php?rid=794776&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688433%26dopt%3DAbstract Authors: Kota P Molecular dynamics simulations have gained importance due to their ability to provide valuable insights into understanding structure-function relationships of biological macromolecules. With increasing computational speeds there has been a substantial demand for optimization of simulation algorithms to obtain results even faster. With this on one hand, the need for ease of operation lies on the other. GUI front end programs are important appurtenances to ease the use of command line programs. Effective use of command line based programs requires basic knowledge of the UNIX shell and at least one of the UNIX based text editors, making it difficult for pure biologists to use them efficiently. GROMACS, a widely used suite of molecular dynamics simulation and analysis progr... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794776 Mon, 13 Aug 2007 12:40:25 +0100 794776 http://www.medworm.com/index.php?rid=794775&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688434%26dopt%3DAbstract Authors: Peres Tde S, Costa FF, Alberto FL We developed a Perl-based tool called LyM to determine the best factor for changes in the expression level for each transcript across two sets of expression libraries. LyM includes a Bayesian framework that analyzes the prior and posterior probability density function for each transcript considering the size of the libraries. To find out the best factor for change in each distribution, LyM was implemented with a binary search. In this work we aimed to validate the performance of LyM tool using SAGE libraries from different human tissues. The results were compared with those generated by DGED (Digital Gene Expression Displayer), which worked as the gold standard, on the same data set, to assess accuracy. SAGE libraries were selected from CGAP f... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794775 Mon, 13 Aug 2007 12:40:25 +0100 794775 http://www.medworm.com/index.php?rid=794774&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688435%26dopt%3DAbstract We describe a coding potential predictor based on artificial neural networks and we compare its performance by using different architectures, learning algorithms and parameters. We rely on a dataset of positive samples constructed from coding sequences and on a negative dataset consisted of all the intergenic regions that were not located between the genes of an operon. Both datasets, positive and negative, were output as fasta formatted files and were used for neural network training. The fast, adaptive, batch learning algorithm Resilient propagation, exhibits the best overall performance on a 64input-10hidden-1output nodes multi-layer perceptron neural network. PMID: 17688435 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794774 Mon, 13 Aug 2007 12:40:25 +0100 794774 http://www.medworm.com/index.php?rid=794773&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688436%26dopt%3DAbstract In this study, we report the identification of the PIP5K coding region in the genome sequence of Eimeria tenella using in silico gene prediction approaches. Prediction of the PIP5K coding sequence was confirmed by mapping the full-length cDNA sequence, generated via the Rapid Amplification of cDNA Ends (RACE) method, to the genomic sequence. The putative PIP5K gene of Eimeria tenella is located on the complementary strand of the E1080B12.b1 contig, and comprises 12 exons. Further analysis showed that the coding region spans from exon 1 to exon 7, with all exons obeying the adopted 'gt..ag' splicing rule of intronic sequences. Consensus of the hexameric 5' donor-splice site was deduced as GTRDBB... and the consensus for the 3' acceptor-splice sites as ...BHDYAG. The gene encodes a 252-amino... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794773 Mon, 13 Aug 2007 12:40:25 +0100 794773 http://www.medworm.com/index.php?rid=794760&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688449%26dopt%3DAbstract Authors: Padhi A, Verghese B, Otta SK, Varghese B, Ramu K The tissue-specific expression and differential function of the crustacean hyperglycemic hormone (CHH) in Carcinus maenas indicate an interesting evolutionary history. Previous studies have shown that CHH from the sinus gland X-organ (XO-type) has hyperglycemic activity, whereas the CHH from the pericardial organ (PO-type) neither shows hyperglycemic activity nor it inhibits Y-organ ecdysteroid synthesis. Here we examined the types of selective pressures operating on the variants of CHH in Carcinus maenas. Maximum likelihood-based codon substitution analyses revealed that the variants of this neuropeptide in C. maenas have been subjected to positive Darwinian selection indicating adaptive evolution and functional divergence amon... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794760 Sat, 16 Jun 2007 04:00:00 +0100 794760 http://www.medworm.com/index.php?rid=794758&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688451%26dopt%3DAbstract Authors: Lim BS, Chong CE, Zamrod Z, Nathan S, Mohamed R Many members of the AraC/XylS family transcription regulator have been proven to play a critical role in regulating bacterial virulence factors in response to environmental stress. By using the Hidden Markov Model (HMM) profile built from the alignment of a 99 amino acid conserved domain sequence of 273 AraC/XylS family transcription regulators, we detected a total of 45 AraC/XylS family transcription regulators in the genome of the Gram-negative pathogen, Burkholderia pseudomallei. Further in silico analysis of each detected AraC/XylS family transcription regulatory protein and its neighboring genes allowed us to make a first-order guess on the role of some of these transcription regulators in regulating important virulence fact... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794758 Sat, 16 Jun 2007 04:00:00 +0100 794758 http://www.medworm.com/index.php?rid=794755&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688454%26dopt%3DAbstract Authors: Ranjan A, Vidyarthi AS, Poddar R To reveal the relative synonymous codon usage and base composition variation in bacteriophages, six mycobacteriophages were used as a model system here and both parameters in these phages and their host bacteria, Mycobacterium tuberculosis, have been determined and compared. As expected for GC-rich genomes, there are predominantly G and C ending codons in all 6 phages. Both Nc plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in the 6 phages. Further analysis indicates that among 6 Mycobacterium phages Che9c, Bxz1 and TM4 may be extremely virulent in nature as most of their genes have high translation efficiency. Based on our data we suggest... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794755 Tue, 12 Jun 2007 04:00:00 +0100 794755 http://www.medworm.com/index.php?rid=794757&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688452%26dopt%3DAbstract Authors: Saha S, Raghava GP This paper describes a method developed for predicting bacterial toxins from their amino acid sequences. All the modules, developed in this study, were trained and tested on a non-redundant dataset of 150 bacterial toxins that included 77 exotoxins and 73 endotoxins. Firstly, support vector machines (SVM) based modules were developed for predicting the bacterial toxins using amino acids and dipeptides composition and achieved an accuracy of 96.07% and 92.50%, respectively. Secondly, SVM based modules were developed for discriminating entotoxins and exotoxins, using amino acids and dipeptides composition and achieved an accuracy of 95.71% and 92.86%, respectively. In addition, modules have been developed for classifying the exotoxins (e. g. activate adenylate... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794757 Mon, 11 Jun 2007 04:00:00 +0100 794757 http://www.medworm.com/index.php?rid=794767&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688442%26dopt%3DAbstract Authors: Ranganath A, Shet KC, Vidyavathi N Structural Genomics initiatives are generating an increasing number of protein structures with very limited biochemical characterization. Characterization of a protein's function and understanding the specific nature of a protein's binding is a critical part of both protein engineering and structure-based drug discovery. The accurate detection of binding site in these protein structures can be valuable in determining its function. As shape plays a crucial role in bimolecular recognition and function, the development of shape analysis techniques is important for understanding protein structure-function relationships. This paper describes the use of the continuous wavelet transforms (CWT) for characterizing shape features of 3D protein structur... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794767 Sat, 09 Jun 2007 04:00:00 +0100 794767 http://www.medworm.com/index.php?rid=794756&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688453%26dopt%3DAbstract Authors: Rajesh R, Gunasekaran K, Muthukumaravel S, Balaraman K, Jambulingam P The voltage-gated sodium channel (VGSC) is the target site for insecticides such as DDT and synthetic pyrethroids. A single base (A-T) change in the knock-down resistance (kdr) allele leads to an amino acid substitution at position 267 that confers the target-mediated resistance to DDT and synthetic pyrethroids in Anopheles gambiae. A theoretical model of the VGSC domain II that contains the site of mutation was constructed using the K+ channel protein of Aeropyrum pernix as a template. The validated model with 88.6% residues in the favored region was subjected to the CASTp program that predicted 30 pockets in the modeled domain II for ligand interaction. In the model, at position 267, leucine was manually r... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794756 Sun, 22 Apr 2007 04:00:00 +0100 794756 http://www.medworm.com/index.php?rid=794768&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688441%26dopt%3DAbstract Authors: Ahmed A, Frey G, Michel CJ Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X , which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i. e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring m... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794768 Wed, 11 Apr 2007 04:00:00 +0100 794768 http://www.medworm.com/index.php?rid=794761&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688448%26dopt%3DAbstract Authors: Idicula-Thomas S, Balaji PV Protein aggregation, being an outcome of improper protein folding, is largely dependent on the folding kinetics of a protein. Previous studies have reported a positive correlation between the stability of the secondary structural elements of a protein and their rate of folding/unfolding. In this in silico study, the secondary and tertiary structures of proteins a) that form inclusion bodies on overexpression in Escherichia coli, b) that form amyloid fibrils and c) that are soluble on overexpression in E. coli are analyzed for certain features that are known to be associated with structural stability. The study revealed that the soluble proteins seem to have a higher rate of folding (based on contact order) and a lower percentage of exposed hydrophob... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794761 Wed, 11 Apr 2007 04:00:00 +0100 794761 http://www.medworm.com/index.php?rid=794759&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688450%26dopt%3DAbstract Authors: Saha S, Raghava GP We have developed a method NTXpred for predicting neurotoxins and classifying them based on their function and origin. The dataset used in this study consists of 582 non-redundant, experimentally annotated neurotoxins obtained from Swiss-Prot. A number of modules have been developed for predicting neurotoxins using residue composition based on feed-forwarded neural network (FNN), recurrent neural network (RNN), support vector machine (SVM) and achieved maximum accuracy of 84.19%, 92.75%, 97.72% respectively. In addition, SVM modules have been developed for classifying neurotoxins based on their source (e.g., eubacteria, cnidarians, molluscs, arthropods have been and chordate) using amino acid composition and dipeptide composition and achieved maximum overall... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794759 Fri, 06 Apr 2007 04:00:00 +0100 794759 http://www.medworm.com/index.php?rid=794762&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688447%26dopt%3DAbstract Authors: Othman R, Wahab HA, Yusof R, Rahman NA Multiple sequence alignment was performed against eight proteases from the Flaviviridae family using ClustalW to illustrate conserved domains. Two sets of prediction approaches were applied and the results compared. Firstly, secondary structure prediction was performed using available structure prediction servers. The second approach made use of the information on the secondary structures extracted from structure prediction servers, threading techniques and DSSP database of some of the templates used in the threading techniques. Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PD... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794762 Tue, 27 Mar 2007 04:00:00 +0100 794762 http://www.medworm.com/index.php?rid=794766&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688443%26dopt%3DAbstract Authors: Mondal S, Babu RM, Bhavna R, Ramakumar S A novel conotoxin pl14a containing 25 amino acid residues with an amidated C-terminus from vermivorous cone snail, Conus planorbis belongs to J-conotoxin superfamily and this is the first conotoxin, which inhibits both nicotinic acetylcholine receptor subtypes and Kv1.6 channel. We have attempted through bioinformatics approaches to elucidate the extent of specificity of pl14a towards Kv1 channel subtypes (Kv1.1-Kv1.6). Our work provides rationale for the relatively high specificity and binding mode of pl14a to Kv1.6 channel.The pl14a peptide contains two types of structural elements, namely the putative dyad (Lys18 and Tyr19) and basic residue ring constituted of arginine residues. We have carried out in silico docking studies so as to... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794766 Mon, 26 Mar 2007 04:00:00 +0100 794766 http://www.medworm.com/index.php?rid=794763&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688446%26dopt%3DAbstract Authors: Grover A, Sharma PC Microsatellites, arrays of 1-6 bp sequences, are abundant in almost all the eukaryotic genomes. Their distribution in the genome is widely accepted to be differential and non random along the axis of the chromosomes. Arabidopsis thaliana genome is dominated by mononucleotide repeats, (A)n being the most abundant motif. In total, 39 microsatellite motifs extended to more than 100 bp in length. Of these, 8 loci are devoid of any gene in their proximity. (AG)n is the most abundant motif among longer repeats. The non-random distribution of microsatellite in the genome is reflected as occurrence of microsatellite clusters in the genome. In total, 3400 microsatellite clusters have been identified in the Arabidopsis genome. Chromosome 2, which is 19.7 Mb long, har... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794763 Mon, 05 Mar 2007 05:00:00 +0100 794763 http://www.medworm.com/index.php?rid=794765&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688444%26dopt%3DAbstract Authors: Srinivasan B, Balaram H PMID: 17688444 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794765 Wed, 28 Feb 2007 05:00:00 +0100 794765 http://www.medworm.com/index.php?rid=794764&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688445%26dopt%3DAbstract Authors: Yao J, Lin H, Doddapaneni H, Civerolo EL The increasing number of whole genomic sequences of microorganisms has led to the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we have developed nWayComp software that compares DNA and protein sequences of phylogenetically-related microorganisms. This package integrates a series of bioinformatics tools such as BLAST, ClustalW, ALIGN, PHYLIP and PRIMER3 for sequence comparison. It searches for homologous sequences among multiple organisms and identifies genes that are unique to a particular organism. The homologous gene sets are then ranked in the ascending order of the sequence similarity. For each set of homologous sequences, a table of sequence identity among... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794764 Wed, 28 Feb 2007 05:00:00 +0100 794764 http://www.medworm.com/index.php?rid=794769&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688440%26dopt%3DAbstract Authors: Gerlach D, Wolf M, Dandekar T, Müller T, Pokorny A, Rahmann S We reconstructed a robust phylogenetic tree of the Metazoa, consisting of almost 1,500 taxa, by profile neighbor joining (PNJ), an automated computational method that inherits the efficiency of the neighbor joining algorithm. This tree supports the one proposed in the latest review on metazoan phylogeny. Our main goal is not to discuss aspects of the phylogeny itself, but rather to point out that PNJ can be a valuable tool when the basal branching pattern of a large phylogenetic tree must be estimated, whereas traditional methods would be computationally impractical. PMID: 17688440 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794769 Sat, 24 Feb 2007 05:00:00 +0100 794769 http://www.medworm.com/index.php?rid=794771&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688438%26dopt%3DAbstract Authors: Negishi Y, Nakamura H, Yachie N, Saito R, Tomita M Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. Here, we present an integrative software platform, eXpanda, which enables an analysis of a very broad range of biological networks, with a special focus on the extraction of characteristic topologies which potentially function as units in the networks. eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory. The results of these analyses are visualizable by vector graphics. eXpanda is under GNU Ge... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794771 Thu, 15 Feb 2007 05:00:00 +0100 794771 http://www.medworm.com/index.php?rid=794770&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688439%26dopt%3DAbstract Authors: Fink JL, Hamilton N Visualization of functional and structural features of biological macromolecules is an important aspect of communicating and analyzing biological data, for example the presence of a transmembrane domain in relation to a nucleotide binding site or the organization of transcription factor binding sites in a promoter. However, this is not necessarily a trivial task especially when the feature information is complex or lengthy. While there are some tools available that can create these images, none have been implemented for the specific purpose of automating the generation of presentation-quality graphics for displaying feature information. We have implemented DomainDraw, a visualization tool that can be used to generate schematic diagrams of biological macromo... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794770 Tue, 13 Feb 2007 05:00:00 +0100 794770 http://www.medworm.com/index.php?rid=794772&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17688437%26dopt%3DAbstract Authors: Gayen K, Gupta M, Venkatesh AK PMID: 17688437 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=794772 Mon, 12 Feb 2007 05:00:00 +0100 794772 http://www.medworm.com/index.php?rid=266462&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789914%26dopt%3DAbstract Authors: Wessel R, Foos V, Aspelmeier A, Jürgens M, Graessmann A, Klein A CorrXpression is a stand-alone desktop application for the identification of significant genes within collections of microarrays. The software combines three methods in two steps of analysis: correspondence analysis (CA), ratio analysis and correlation analysis. The graphical interface of CorrXpression visualizes the result of the CA with a biplot and the expression of selected genes in dependency of the experiments as bar diagrams. The CA-plot is an excellent tool for visualization and evaluation of data and results of ratio analysis and correlation analysis. The input data are selected from a database or from appropriate ASCII files. PMID: 16789914 [PubMed - indexed for MEDLINE] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=266462 Wed, 08 Nov 2006 15:11:02 +0100 266462 http://www.medworm.com/index.php?rid=266461&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789918%26dopt%3DAbstract In this study, an attempt has been made to develop a method for predicting weak hydrogen bonding interactions, namely, C alpha-H...O and C alpha-H...pi interactions in proteins using artificial neural network. Both standard feed-forward neural network (FNN) and recurrent neural networks (RNN) have been trained and tested using five-fold cross-validation on a non-homologous dataset of 2298 protein chains where no pair of sequences has more than 25% sequence identity. It has been found that the prediction accuracy varies with the separation distance between donor and acceptor residues. The maximum sensitivity achieved with RNN for C alpha-H...O is 51.2% when donor and acceptor residues are four residues apart (i.e. at delta D-A = 4) and for C alpha-H...pi is 82.1% at delta D-A = 3. The perfo... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=266461 Wed, 08 Nov 2006 15:11:02 +0100 266461 http://www.medworm.com/index.php?rid=107233&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972006%26dopt%3DAbstract Authors: Michael H, Chen X, Fricke E, Haubrock M, Ricanek R, Wingender E CYTOMER is a relational database of organs/tissues, cell types, physiological systems and developmental stages that currently focuses on the human system. From this database, we have derived an ontology for anatomical and morphological structures for the human organism which includes all embryonal stages and the cell types constituting these structures. The ontology has been transferred to the OWL format and is freely available for download at http://cytomer/bioinf.med.uni-goettingen.de. PMID: 15972006 [PubMed - indexed for MEDLINE] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107233 Tue, 18 Jul 2006 17:26:33 +0100 107233 http://www.medworm.com/index.php?rid=154178&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922697%26dopt%3DAbstract Authors: Escobar AJ, Arenas AF, Gomez-Marin JE The serine-rich (SR) protein family is involved in the pre-mRNA splicing process and the DNA sequences of the corresponding genes are highly conserved in the metazoan organisms. The mammalian SR proteins consist of one or two characteristic RNA binding domains (RBD), containing the signature sequences RDAEDA and SWQDLKD and a RS (arginine/serine-rich) domain. We used the amino acid and nucleotide sequences deposited in GenBank and Swiss-Prot databases to perform a phylogenetic analysis using bioinformatics tools. The results of the phylogenetic trees suggest that this family has evolved by several gene duplication events as a result of a positive selection mechanism. PMID: 16922697 [PubMed - as supplied by publisher] (Source: In Silico... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154178 Thu, 22 Jun 2006 06:00:00 +0100 154178 http://www.medworm.com/index.php?rid=154179&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922696%26dopt%3DAbstract Authors: Chong CE, Lim BS, Nathan S Recent advances in DNA sequencing technology have enabled elucidation of whole genome information from a plethora of organisms. In parallel with this technology, various bioinformatics tools have driven the comparative analysis of the genome sequences between species and within isolates. While drawing meaningful conclusions from a large amount of raw material, computer-aided identification of suitable targets for further experimental analysis and characterization, has also led to the prediction of non-human homologous essential genes in bacteria as promising candidates for novel drug discovery. Here, we present a comparative genomic analysis to identify essential genes in Burkholderia pseudomallei. Our in silico prediction has identified 312 essentia... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154179 Mon, 19 Jun 2006 06:00:00 +0100 154179 http://www.medworm.com/index.php?rid=154195&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922680%26dopt%3DAbstract Authors: Anwar T, Lal SK, Khan AU The avian influenza (bird flu) is an infectious disease of birds, ranging from a mild to a severe form of illness. Influenza viruses pose significant challenges to both human and animal health. The proteins, nucleoprotein (NP), neuraminidase (NA) and hemagglutinin (HA) of influenza A virus (Bird flu virus) sub-type A/Hatay/2004/(H5N1) from chicken were selected for this study. Our in silico analysis predicted that HA of influenza A virus is highly sensitive to mutations and hence it is significant for its pathogenic nature. None of the mutations was detected as an important change except in NA where K332R was at a PKC phosphorylation site. Analysis of the sequence comparison showed that the maximum number of mutations were observed in HA. These mutatio... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154195 Sat, 17 Jun 2006 06:00:00 +0100 154195 http://www.medworm.com/index.php?rid=154183&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922692%26dopt%3DAbstract Authors: Merkl R In order to identify and to characterise gene clusters conserved in microbial genomes, the algorithm AMIGOS was developed. It is based on a categorisation of genes using a predefined set of gene functions (GFs). After the categorisation of all genes of a genome and based on their location on a replicon, distances between GFs were determined and stored in genome-specific matrices. These matrices were used to identify GF clusters like those strictly conserved in 13 archaeal, in 47 bacterial genomes and in the combination of the sets. Within the combined set of these 60 microbial genomes, there exist only two strictly conserved clusters harbouring two ribosomal genes each, namely those for L4, L23 and L22, L29. In order to characterise less strictly conserved GF clusters,... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154183 Sat, 17 Jun 2006 06:00:00 +0100 154183 http://www.medworm.com/index.php?rid=154181&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922694%26dopt%3DAbstract Authors: Chakrabarti S, Manohari G, Pugalenthi G, Sowdhamini R The presence of sequence homologues and the availability of structural information of proteins enable better understanding of the biological function of a protein family. A majority of entries in protein structural databank are single member superfamilies for which it is hard to derive motifs due to the paucity of structural homologues. Important conserved segments for these superfamilies have been identified and compiled into a database, SSToSS (Sequence Structural Templates of Single member Superfamily). Conserved regions, recognized by permitted amino acid exchanges, are mapped on the structure and various structural features (solvent accessibility, secondary structure content, hydrogen bonding and residue packing) are e... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154181 Thu, 08 Jun 2006 06:00:00 +0100 154181 http://www.medworm.com/index.php?rid=154180&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922695%26dopt%3DAbstract Authors: Blackshields G, Wallace IM, Larkin M, Higgins DG The most popular way of comparing the performance of multiple sequence alignment programs is to use empirical testing on sets of test sequences. Several such test sets now exist, each with potential strengths and weaknesses. We apply several different alignment packages to 6 benchmark datasets, and compare their relative performances. HOMSTRAD, a collection of alignments of homologous proteins, is regularly used as a benchmark for sequence alignment though it is not designed as such, and lacks annotation of reliable regions within the alignment. We introduce this annotation into HOMSTRAD using protein structural superposition. Results on each database show that method performance is dependent on the input sequences. Alignment be... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154180 Thu, 08 Jun 2006 06:00:00 +0100 154180 http://www.medworm.com/index.php?rid=154184&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922691%26dopt%3DAbstract Authors: Sakharkar MK, Kangueane P, Sakharkar KR, Zhong Z Protein lengths vary considerably from a few to thousands of amino acids and length variations are documented to have multiple effects. A computational approach to investigate the functional impact of protein length variation in genetic disorders is presented. The genes for huge proteins are found to have more introns. Our analysis also shows greater involvement of huge proteins in hereditary diseases. PMID: 16922691 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154184 Sat, 03 Jun 2006 06:00:00 +0100 154184 http://www.medworm.com/index.php?rid=154182&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922693%26dopt%3DAbstract Authors: Su G, Mao B, Wang J We have implemented a novel gapped-alignment algorithm to compare Position Frequency Matrices (PFM) for Transcription Factor Binding Sites. The application compares an input PFM with those collected from public databases and outputs similarity scores, sequence alignments and related PFM clusters. MACO is freely accessible on a web server located at www.nicemice.cn/bioinfo/MACO. Source code is distributed upon request to the authors. PMID: 16922693 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154182 Mon, 29 May 2006 06:00:00 +0100 154182 http://www.medworm.com/index.php?rid=154191&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922684%26dopt%3DAbstract Authors: Nair AS, Mahalakshmi T This paper reports a novel symbol-to-signal mapping for DNA sequences, based on the concept of categorical periodograms. A categorical periodogram is a numeric sequence with the n-th element of the sequence indicating the number of occurrences of cycles with period n in it. The period of the cycle is defined as the number of intervening events plus one. Spectral analysis studies have been conducted on Cumulative Categorical Periodogram (CCP) of 10 genes from the data set of Burset and Guigo. It is observed that the spectral signatures in CCP are functionally equivalent to the established N/3 peak in the spectrum of indicator sequences of genomes. Being a single sequence compared to four sequences in the case of indicator sequence representation, the meth... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154191 Sat, 20 May 2006 06:00:00 +0100 154191 http://www.medworm.com/index.php?rid=154185&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922690%26dopt%3DAbstract Authors: Massey SE Three aminoacyl-tRNA synthetases from yeast, one from plants and one from mammals possess unusual structures at their N termini, namely ? helices with basic residues distributed asymmetrically, on a single face of the helix. It is unknown if these 'basic faced' alpha helices (BFAHs) are unique to the aminoacyl-tRNA synthetases. Analysis of the amino acid sequences of these five aminoacyl-tRNA synthetases using the hydrophobic moment algorithm failed to accurately identify the BFAHs. A new algorithm was therefore developed, called the 'basic moment'. This is a Fourier analysis procedure that predicts the distribution of basic residues within protein secondary structure. The basic moment identifies with a high degree of accuracy the five known BFAHs and also identifies... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154185 Sat, 06 May 2006 06:00:00 +0100 154185 http://www.medworm.com/index.php?rid=154192&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922683%26dopt%3DAbstract We present a simple ordinary differential equation (ODE) model of the adaptive response to an osmotic shock in the yeast Saccharomyces cerevisiae. The model consists of two main components. First, a biophysical model describing how the cell volume and the turgor pressure are affected by varying extra-cellular osmolarity. The second component describes how the cell controls the biophysical system in order to keep turgor pressure, or equivalently volume, constant. This is done by adjusting the glycerol production and the glycerol outflow from the cell. The complete model consists of 4 ODEs, 3 algebraic equations and 10 parameters. The parameters are constrained from various literature sources and estimated from new and previously published absolute time series data on intra-cellular and tota... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154192 Sat, 29 Apr 2006 06:00:00 +0100 154192 http://www.medworm.com/index.php?rid=154193&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922682%26dopt%3DAbstract Authors: Bankhead Iii A, Magnuson NS, Heckendorn RB A G2/M genetic network simulation is trained with tumor incidence data from knockout experiments. The genetic network is implemented using a neural network; knockout genotypes are simulated by removing nodes in the neural network. Two analyses are used to interpret the resulting network weights. We use a novel approach of fixing the network topology that allows knockout TSG (tumor suppressor gene) data from multiple studies to overlap and indirectly inform one another. The trained simulation is validated by reproducing qualitative mammary cancer susceptibilities of ATM, BRCA1, and p53 TSGs. The work described is valuable because it allows TSG mammary cancer susceptibility to be quantified using genetic network topology and in vivo kno... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154193 Sat, 22 Apr 2006 06:00:00 +0100 154193 http://www.medworm.com/index.php?rid=154187&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922688%26dopt%3DAbstract Authors: Buelow L, Steffens NO, Galuschka C, Schindler M, Hehl R AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of th... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154187 Fri, 21 Apr 2006 06:00:00 +0100 154187 http://www.medworm.com/index.php?rid=154186&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922689%26dopt%3DAbstract Authors: Piva F, Principato G Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length an... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154186 Thu, 20 Apr 2006 06:00:00 +0100 154186 http://www.medworm.com/index.php?rid=154189&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922686%26dopt%3DAbstract Authors: Balamurugan B, Roshan MN, Michael D, Ambaree M, Divya S, Keerthana H, Seemanthini M, Sekar K Structure prediction methods aim to identify the relationship between the amino acid sequence of an unknown protein and information comprised in databases of known protein structures. Towards this end, we created a database by combining the amino acid sequences and the corresponding three-dimensional atomic coordinates for all the 25% non-redundant protein chains available in the Protein Data Bank. It contains information about the peptide fragments that are 5 to 10 residues long. In addition, options are provided for the users to visualize the individual motifs and the superposed fragments in the client machine. Further, useful functionalities are provided to look for similar sequence... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154189 Wed, 19 Apr 2006 06:00:00 +0100 154189 http://www.medworm.com/index.php?rid=154194&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922681%26dopt%3DAbstract Authors: Kiranmayi P, Mohan PM Neurospora crassa has been the model filamentous fungus for the study of many fundamental cellular mechanisms of transport and metabolism. The recently completed genome sequence of N. crassa has over 10,000 genes without significant matches for a large number of genes (41%) in the sequence databases, indeed presents many challenges for new discoveries. Using transporter database and BLAST searches a total of 65 open reading frames for putative cation transporter genes have been identified in N. crassa. These were further confirmed by characteristic features of the family like transmembrane domains (TOPPRED 2), conserved motifs (Clustal W) and phylogenetic analysis (TREETOP). In Neurospora cation transporter genes constitute nearly 18.3% of the total membr... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154194 Mon, 17 Apr 2006 06:00:00 +0100 154194 http://www.medworm.com/index.php?rid=154190&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922685%26dopt%3DAbstract Authors: Bose M, Barber RD Prophage loci often remain under-annotated or even unrecognized in prokaryotic genome sequencing projects. A PHP application, Prophage Finder, has been developed and implemented to predict prophage loci, based upon clusters of phage-related gene products encoded within DNA sequences. This application provides results detailing several facets of these clusters to facilitate rapid prediction and analysis of prophage sequences. Prophage Finder was tested using previously annotated prokaryotic genomic sequences with manually curated prophage loci as benchmarks. Additional analyses from Prophage Finder searches of several draft prokaryotic genome sequences are available through the Web site (http://bioinformatics.uwp.edu/~phage/DOEResults.php) to illustrate the po... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154190 Sat, 15 Apr 2006 06:00:00 +0100 154190 http://www.medworm.com/index.php?rid=154188&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922687%26dopt%3DAbstract This study provides insight into the structure of eukaryotic genes. These results confirm and expand the previously identified regulatory potential of first exons and introns. PMID: 16922687 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=154188 Fri, 14 Apr 2006 06:00:00 +0100 154188 http://www.medworm.com/index.php?rid=107172&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789921%26dopt%3DAbstract Authors: Mizuta S, Munakata H, Aimaiti A, Oya I, Oosawa K, Shimizu T High sequence identity between two proteins (e. g. >60%) is a strong evidence for high structural similarity. However, internal shifts in one of the two proteins can sometimes give rise to unexpectedly high structural differences. This, in turn, causes unreliable structure predictions when two such proteins are used in homology modeling. Here, we perform a computational analysis of helix shifts and we show that their occurrence can be predicted with statistical learning methods. Our results indicate that helix shifts increase the RMS error by factor 2.6 compared to those protein pairs without a helix shift. Although helix shifts are rare (1.6% of helices and a commensurately higher number of proteins are affected),... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107172 Fri, 10 Mar 2006 07:00:00 +0100 107172 http://www.medworm.com/index.php?rid=107175&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789918%26dopt%3DAbstract In this study, an attempt has been made to develop a method for predicting weak hydrogen bonding interactions, namely, C-alpha-H...O and C-alpha-H...pi interactions in proteins using artificial neural network. Both standard feed-forward neural network (FNN) and recurrent neural networks (RNN) have been trained and tested using five-fold cross-validation on a non-homologous dataset of 2298 protein chains where no pair of sequences has more than 25% sequence identity. It has been found that the prediction accuracy varies with the separation distance between donor and acceptor residues. The maximum sensitivity achieved with RNN for C-alpha-H...O is 51.2% when donor and acceptor residues are four residues apart (i. e. at deltaD-A = 4) and for C-alpha-H...? is 82.1% at deltaD-A = 3. The perform... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107175 Wed, 01 Mar 2006 07:00:00 +0100 107175 http://www.medworm.com/index.php?rid=107173&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789920%26dopt%3DAbstract Authors: Bock C, Hesser J High sequence identity between two proteins (e. g. >60%) is a strong evidence for high structural similarity. However, internal shifts in one of the two proteins can sometimes give rise to unexpectedly high structural differences. This, in turn, causes unreliable structure predictions when two such proteins are used in homology modeling. Here, we perform a computational analysis of helix shifts and we show that their occurrence can be predicted with statistical learning methods. Our results indicate that helix shifts increase the RMS error by factor 2.6 compared to those protein pairs without a helix shift. Although helix shifts are rare (1.6% of helices and a commensurately higher number of proteins are affected), they therefore pose a significant problem ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107173 Wed, 01 Mar 2006 07:00:00 +0100 107173 http://www.medworm.com/index.php?rid=107174&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789919%26dopt%3DAbstract Authors: Seshasayee AS Protein-protein interaction networks are useful in contextual annotation of protein function and in general to achieve a system-level understanding of cellular behavior. This work reports on the social behavior of the yeast protein-protein interaction network and concludes that it is non-random. This work, while providing an analysis of organization of genes into functional societies, can potentially be useful in assessing the accuracy of contextual gene annotation based on such interaction networks. PMID: 16789919 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107174 Wed, 22 Feb 2006 07:00:00 +0100 107174 http://www.medworm.com/index.php?rid=107176&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789917%26dopt%3DAbstract Authors: Gambin A, Lasota S, Rutkowski M We introduce and formally define the notion of a stationary state for Petri nets. We also propose a fully automatic method for finding such states. The procedure makes use of the Presburger arithmetic to describe all the stationary states. Finally we apply this novel approach to find stationary states of a gene regulatory network describing the flower morphogenesis of A. thaliana. This shows that the proposed method can be successfully applied in the study of biological systems. PMID: 16789917 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107176 Sun, 19 Feb 2006 07:00:00 +0100 107176 http://www.medworm.com/index.php?rid=107178&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789915%26dopt%3DAbstract In this study, we generalize this approach and analyze correlation functions of longer motifs such as tetramers or poly(A) sequences. Periodically placed motifs may indicate regular protein binding or curvature signals. We detected various periodic signals e. g. strong 10-11 bp oscillations of periodically placed poly(A), poly(T) or poly(W) stretches. These observations lead to a new view on the intensively studied 10-11 bp periodicities. PMID: 16789915 [PubMed - as supplied by publisher] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107178 Sat, 11 Feb 2006 07:00:00 +0100 107178 http://www.medworm.com/index.php?rid=107177&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789916%26dopt%3DAbstract Authors: Komura D, Nishimura K, Ishikawa S, Panda B, Huang J, Nakamura H, Ihara S, Hirose M, Jones KW, Aburatani H Genomic copy number change is one of the important phenomenon observed in cancer and other genetic disorders. Recently oligonucleotide microarrays have been used to analyze changes in the copy number. Although high density microarrays provide genome wide useful data on copy number, they are often associated with substantial amount of experimental noise that could affect the performance of the analyses. We used the high density oligonucleotide genotyping microarrays in our experiments that uses redundant probe tiling approach for individual SNPs. We found that the noise in the genotyping microarray data is associated with several experimental steps during target preparation... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107177 Sat, 11 Feb 2006 07:00:00 +0100 107177 http://www.medworm.com/index.php?rid=107179&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789914%26dopt%3DAbstract Authors: Wessel R, Foos V, Aspelmeier A, Juergens M, Graessmann A, Klein A CorrXpression is a stand-alone desktop application for the identification of significant genes within collections of microarrays. The software combines three methods in two steps of analysis: correspondence analysis (CA), ratio analysis and correlation analysis. The graphical interface of CorrXpression visualizes the result of the CA with a biplot and the expression of selected genes in dependency of the experiments as bar diagrams. The CA-plot is an excellent tool for visualization and evaluation of data and results of ratio analysis and correlation analysis. The input data are selected from a database or from appropriate ASCII files. PMID: 16789914 [PubMed - as supplied by publisher] (Source: In Silico Bio... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107179 Sat, 04 Feb 2006 07:00:00 +0100 107179 http://www.medworm.com/index.php?rid=107180&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789913%26dopt%3DAbstract In this report we developed the Gene Prediction Accuracy Classification (GPAC) test, which provides statistical evidence of sensitivity by repeating the same analysis for five different gene groups (classified according to annotation accuracy level), and for randomly sampled gene groups, with the same number of genes as each of the five classified groups. Variability in these results is then assessed, and if the results vary significantly with different data subsets, the analysis is considered "sensitive" to annotation completeness, and careful selection of data is advised prior to the actual in silico analysis. The GPAC test has been applied to the analyses of Sakai et al., 2001, and Ohno et al., 2001, and it revealed that the analysis of Ohno et al. was more sensitive to annotation compl... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107180 Thu, 02 Feb 2006 07:00:00 +0100 107180 http://www.medworm.com/index.php?rid=107183&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789910%26dopt%3DAbstract Authors: Konieczny L, Brylinski M, Roterman I The model adopting the three-dimensional Gauss function to express the hydrophobicity distribution in proteins is presented in this paper. The tendency to create the hydrophobic center during protein folding is expressed in form of an external force field of the form of three-dimensional Gauss function which directs the folding polypeptide to locate the hydrophobic residues in a central part of the molecule and hydrophilic ones exposed toward the molecular surface. The decrease of the differences between hydrophobicity distribution as it appears at each step of the folding simulation and the expected hydrophobicity distribution (three-dimensional Gauss function) is the convergence criterion together with traditional non-bonding interaction ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107183 Mon, 23 Jan 2006 07:00:00 +0100 107183 http://www.medworm.com/index.php?rid=107184&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789909%26dopt%3DAbstract Authors: Doi A, Nagasaki M, Matsuno H, Miyano S MDM2 and p19ARF are essential proteins in cancer pathways forming a complex with protein p53 to control the transcriptional activity of protein p53. It is confirmed that protein p53 loses its transcriptional activity by forming the functional dimer with protein MDM2. However, it is still unclear that protein p53 keeps its transcriptional activity when it forms the trimer with proteins MDM2 and p19ARF. We have observed mutual behaviors among genes p53, MDM2, p19ARF and their products on a computational model with hybrid functional Petri net (HFPN) which is constructed based on information described in the literature. The simulation results suggested that protein p53 should have the transcriptional activity in the forms of the trimer of pro... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107184 Wed, 04 Jan 2006 07:00:00 +0100 107184 http://www.medworm.com/index.php?rid=107182&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789911%26dopt%3DAbstract Authors: Matute DR, Barreto-Hernandez E, Falquet L Automatically finding new protein domains is a challenge when using the complete collection of known proteins (i. e., UniProt). By limiting the taxonomic range to class insecta, including two full proteomes (A. gambiae and D. melanogaster), we reduced the size of the search space in the hope of finding taxon-specific domains. The MKDOM2 program (http://prodes.toulouse.inra.fr/prodom/xdom/mkdom2.html) was used to cluster the insect proteins into potential domains that were analyzed manually in a second step. We analyzed 219 potential domains, of which 2 were insect-specific. We show that it is possible to find new domains or to extend known domains using a semi-automated method; however the goal to detect class-specific domains was only... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107182 Tue, 03 Jan 2006 07:00:00 +0100 107182 http://www.medworm.com/index.php?rid=107181&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789912%26dopt%3DAbstract Authors: Dutta A, Singh SK, Ghosh P, Mukherjee R, Mitter S, Bandyopadhyay D Availability of genome sequences of pathogens has provided a tremendous amount of information that can be useful in drug target and vaccine target identification. One of the recently adopted strategies is based on a subtractive genomics approach, in which the subtraction dataset between the host and pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used successfully in recent times to identify essential genes in Pseudomonas aeruginosa. We have used the same methodology to analyse the whole genome sequence of the human gastric pathogen Helicobacter pylori. Our analysis revealed that out of the 1590 coding sequenc... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107181 Tue, 03 Jan 2006 07:00:00 +0100 107181 http://www.medworm.com/index.php?rid=410318&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274764%26dopt%3DAbstract Authors: Reddy CS, Manonmani A, Babu M, Sowdhamini R Domain finding algorithms are useful to understand overall domain architecture and to propose biological function to gene products. Automated methods of applying these tools to large-scale genome studies often employ stringent thresholds to recognize sequence domains. The realization of additional domains can be tedious involving manual intervention but can lead to better understanding of overall biological function. We propose a multi-step approach for the further examination of unassigned linker regions that exploits properties such as the conservation of domain architectures of homologous proteins to propose connections. Improved structure prediction is possible starting from initial domain architectures, obtained from simple 'dom... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410318 Sun, 01 Jan 2006 07:00:00 +0100 410318 http://www.medworm.com/index.php?rid=410317&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274765%26dopt%3DAbstract Authors: Faria-Campos AC, Campos SV, Prosdocimi F, Franco GC, Franco GR, Ortega JM The use of sequences from specific organisms for annotation requires that it does not represent great loss of information and that the sequences available suffice for annotation. In order to investigate whether or not sequences from model organisms may suffice for annotation of sequences from the trematode Schistosoma mansoni, we performed local BLAST searches of S. mansoni sequences against other organisms sequences present in the NCBI database nr. Results have been inserted into a relational database and hits to sequences from three model organisms, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens have been computed and compared to hits to sequences from other organisms present in nr; s... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410317 Sun, 01 Jan 2006 07:00:00 +0100 410317 http://www.medworm.com/index.php?rid=410316&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274766%26dopt%3DAbstract Authors: Shil P, Dudani N, Vidyasagar PB Sequence based homology studies play an important role in evolutionary tracing and classification of proteins. Various methods are available to analyze biological sequence information. However, with the advent of proteomics era, there is a growing demand for analysis of huge amount of biological sequence information, and it has become necessary to have programs that would provide speedy analysis. ISHAN has been developed as a homology analysis package, built on various sequence analysis tools viz FASTA, ALIGN, CLUSTALW, PHYLIP and CODONW (for DNA sequences). This JAVA application offers the user choice of analysis tools. For testing, ISHAN was applied to perform phylogenetic analysis for sets of Caspase 3 DNA sequences and NF-kappaB p105 amino a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410316 Sun, 01 Jan 2006 07:00:00 +0100 410316 http://www.medworm.com/index.php?rid=410315&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274767%26dopt%3DAbstract Authors: Ahram M, Litou ZI, Fang R, Al-Tawallbeh G Genomics and proteomics have added valuable information to our knowledgebase of the human biological system including the discovery of therapeutic targets and disease biomarkers. However, molecular profiling studies commonly result in the identification of novel proteins of unknown localization. A class of proteins of special interest is membrane proteins, in particular plasma membrane proteins. Despite their biological and medical significance, the 3-dimensional structures of less than 1% of plasma membrane proteins have been determined. In order to aid in identification of membrane proteins, a number of computational methods have been developed. These tools operate by predicting the presence of transmembrane segments. Here, we utiliz... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410315 Sun, 01 Jan 2006 07:00:00 +0100 410315 http://www.medworm.com/index.php?rid=410314&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274768%26dopt%3DAbstract Authors: Davis MJ, Zhang F, Yuan Z, Teasdale RD Membrane organization describes the relationship of proteins to the membrane, that is, whether the protein crosses the membrane or is integral to the membrane and its orientation with respect to the membrane. Membrane organization is determined primarily by the presence of two features which target proteins to the secretory pathway: the endoplasmic reticulum signal peptide and the ?-helical transmembrane domain. In order to generate membrane organization annotation of high quality, confidence and throughput, the Membrane Organization (MemO) pipeline was developed, incorporating consensus feature prediction modules with integration and annotation rules derived from biological observations. The pipeline classifies proteins into six categori... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410314 Sun, 01 Jan 2006 07:00:00 +0100 410314 http://www.medworm.com/index.php?rid=410313&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274769%26dopt%3DAbstract Authors: Chopra P, Kamma A Synthetic Biology is a field involving synthesis of novel biological systems which are not generally found in nature. It has brought a new paradigm in science as it has enabled scientists to create life from the scratch, hence helping better understand the principles of biology. The viability of living organisms that use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. The field holds a promise for mass production of cheap drugs and programming bacteria to seek-and-destroy tumors in the body. However, the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical chal... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410313 Sun, 01 Jan 2006 07:00:00 +0100 410313 http://www.medworm.com/index.php?rid=410312&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274770%26dopt%3DAbstract Authors: Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A In the archaea, some tRNA precursors contain intron(s) not only in the anticodon loop region but also in diverse sites of the gene (intron-containing tRNA or cis-spliced tRNA). The parasite Nanoarchaeum equitans, a member of the Nanoarchaeota kingdom, creates functional tRNA from separate genes, one encoding the 5'-half and the other the 3'-half (split tRNA or trans-spliced tRNA). Although recent genome projects have revealed a huge amount of nucleotide sequence data in the archaea, a comprehensive methodology for intron-containing and split tRNA searching is yet to be established. We therefore developed SPLITS, which is aimed at searching for any type of tRNA gene and is especially focused on intron-containin... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410312 Sun, 01 Jan 2006 07:00:00 +0100 410312 http://www.medworm.com/index.php?rid=410311&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274771%26dopt%3DAbstract Authors: Doderer M, Yoon K, Salinas J, Kwek S In silico prediction of protein subcellular localization based on amino acid sequence can reveal valuable information about the protein's innate roles in the cell. Unfortunately, such prediction is made difficult because of complex protein sorting signals. Some prediction methods are based on searching for similar proteins with known localization, assuming that known homologs exist. However, it may not perform well on proteins with no known homolog. In contrast, machine learning-based approaches attempt to infer a predictive model that describes the protein sorting signals. Alas, in doing so, it does not take advantage of known homologs (if they exist) by doing a simple "table lookup". Here, we capture the best of both worlds by combining b... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410311 Sun, 01 Jan 2006 07:00:00 +0100 410311 http://www.medworm.com/index.php?rid=410310&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274772%26dopt%3DAbstract Authors: Librando V, Gullotto D, Minniti Z This paper presents a computer aided design method useful for simulation of a set of proteolytic cleavages upon target proteins obtained from the Brookhaven Data Bank. The method was developed by using algorithms that are able to interface themselves with other software environments, in order to assist computer analyses in the molecular modelling field, and allowing the generation of molecular libraries containing protein fragments produced by simulated proteolysis. These libraries include structures that differ for several amino acid deletions upon specified regions of the primary sequence. Target residues chosen for the simulation are compatible with enzymatic proteolysis methods used in conventional laboratory procedures. Furthermore, algor... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410310 Sun, 01 Jan 2006 07:00:00 +0100 410310 http://www.medworm.com/index.php?rid=410309&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274773%26dopt%3DAbstract Authors: Sekhar PN, Kishor PB, Reddy LA, Mondal P, Dash AK, Kar M, Mohanty S, Sabat SC Homology modeling of the catalase, CatC cloned and sequenced from rice (Oryza sativa L., cv Ratna an Indica cultivar) has been performed based on the crystal structure of the catalase CatF (PDB code 1m7s) by using the software MODELLER. With the aid of molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and VERIFY - 3D graph, which show that the final refined model is reliable. With this model, a flexible docking study with the hydrogen peroxide, the substrate for catalase, is performed and the results indicate that Arg310, Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bond... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410309 Sun, 01 Jan 2006 07:00:00 +0100 410309 http://www.medworm.com/index.php?rid=410308&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17274774%26dopt%3DAbstract We describe an attempt to design better antibiotics on the basis of a computer-aided simulation of the interaction between a drug and its target molecule. PMID: 17274774 [PubMed - in process] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=410308 Sun, 01 Jan 2006 07:00:00 +0100 410308 http://www.medworm.com/index.php?rid=216920&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17009421%26dopt%3DAbstract In this study, we searched for tandem repeats (TRs) in 44 prokaryotic genomes by the color-coding method and sought the signs of genome rearrangements by detailed analysis of the detected TRs. We found 13,542 tandem repeats from 44 prokaryotic genomes in total ranging from several tens to one thousand per genome. The results of statistical analysis show that TRs tend to exist on high base composition bias regions in some genomes. Moreover, we recognized the characteristic distribution patterns of equivalent TR-pairs in 12 genomes, which are expected to indicate the occurrence of whole-genome duplication (WGD) on the genomes. It is demonstrated that TRs could indeed be used for seeking genome rearrangements. Although it has not been made clear at this time whether or not WGD had occurred in... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=216920 Sun, 01 Jan 2006 07:00:00 +0100 216920 http://www.medworm.com/index.php?rid=449981&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16922694%26dopt%3DAbstract Authors: Chakrabarti S, Manohari G, Pugalenthi G, Sowdhamini R The presence of sequence homologues and the availability of structural information of proteins enable better understanding of the biological function of a protein family. A majority of entries in protein structural databank are single member superfamilies for which it is hard to derive motifs due to the paucity of structural homologues. Important conserved segments for these superfamilies have been identified and compiled into a database, SSToSS (Sequence Structural Templates of Single member Superfamily). Conserved regions, recognized by permitted amino acid exchanges, are mapped on the structure and various structural features (solvent accessibility, secondary structure content, hydrogen bonding and residue packing) are e... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=449981 Sun, 01 Jan 2006 05:00:00 +0100 449981 http://www.medworm.com/index.php?rid=107185&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16789908%26dopt%3DAbstract Authors: Khan IA, Mort M, Buckland PR, O'donovan MC, Cooper DN, Chuzhanova NA DNA sequence features were sought that could be used for the in silico ascertainment of the likely functional consequences of single nucleotide changes in human gene promoter regions. To identify relevant features of the local DNA sequence context, we transformed into consensus tables the nucleotide composition of sequences flanking 101 promoter SNPs of type C?T or A?G, defined empirically as being either 'functional' or 'non-functional' on the basis of a standardised reporter gene assay. The similarity of a given sequence to these consensus tables was then measured by means of the Shapiro-Senapathy score. A decision rule with the potential to discriminate between empirically ascertained functional and non-fu... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=107185 Tue, 27 Dec 2005 07:00:00 +0100 107185 http://www.medworm.com/index.php?rid=117963&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972001%26dopt%3DAbstract Authors: Lee V, Camon E, Dimmer E, Barrell D, Apweiler R The number of large-scale experimental datasets generated from high-throughput technologies has grown rapidly. Biological knowledge resources such as the Gene Ontology Annotation (GOA) database, which provides high-quality functional annotation to proteins within the UniProt Knowledgebase, can play an important role in the analysis of such data. The integration of GOA with analytical tools has proved to aid the clustering, annotation and biological interpretation of such large expression datasets. GOA is also useful in the development and validation of automated annotation tools, in particular text-mining systems. The increasing interest in GOA highlights the great potential of this freely available resource to assist both the bi... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117963 Sat, 01 Jan 2005 07:00:00 +0100 117963 http://www.medworm.com/index.php?rid=117962&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972002%26dopt%3DAbstract Authors: Koike A, Takagi T With the exponentially increasing amount of information in the biomedical field, the significance of advanced information retrieval and information extraction, as well as the role of databases, has been increasing. PRIME is an integrated gene/protein informatics database based on natural language processing. It provides automatically extracted protein/family/gene/compound interaction information including both physical and genetic interactions, gene ontology based functions, and graphic pathway viewers. Gene/protein/family names and functional terms are recognized based on dictionaries developed in our laboratory. The interaction and functional information are extracted by syntactic dependencies and various phrase patterns. We have included about 920,000 (non... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117962 Sat, 01 Jan 2005 07:00:00 +0100 117962 http://www.medworm.com/index.php?rid=117961&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972003%26dopt%3DAbstract We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/ PMID: 15972003 [PubMed - indexed for MEDLINE] (Source: In Silico Biol) In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117961 Sat, 01 Jan 2005 07:00:00 +0100 117961 http://www.medworm.com/index.php?rid=117960&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972004%26dopt%3DAbstract Authors: Lefranc MP, Clement O, Kaas Q, Duprat E, Chastellan P, Coelho I, Combres K, Ginestoux C, Giudicelli V, Chaume D, Lefranc G IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of term... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117960 Sat, 01 Jan 2005 07:00:00 +0100 117960 http://www.medworm.com/index.php?rid=117959&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972005%26dopt%3DAbstract Authors: Saric J, Jensen LJ, Rojas I This paper presents an approach using syntactosemantic rules for the extraction of relational information from biomedical abstracts. The results show that by overcoming the hurdle of technical terminology, high precision results can be achieved. From abstracts related to baker's yeast, we manage to extract a regulatory network comprised of 441 pairwise relations from 58,664 abstracts with an accuracy of 83 - 90%. To achieve this, we made use of a resource of gene/protein names considerably larger than those used in most other biology related information extraction approaches. This list of names was included in the lexicon of our retrained partof- speech tagger for use on molecular biology abstracts. For the domain in question an accuracy of 93.6 - 9... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117959 Sat, 01 Jan 2005 07:00:00 +0100 117959 http://www.medworm.com/index.php?rid=117958&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972007%26dopt%3DAbstract In this study, we report our approach to dictionary building and term matching in biomedical texts. Large amount of terms with/without part-of-speech (POS) and/or category information were gathered, and a completion program generated approximately 1.36 million term variants to avoid stemming problems when matching terms. The dictionary was stored in a relational database management system (RDBMS) for quick lookup, and used by a matching program. Since the matching operation is not restricted to a substring surrounded by space characters, we can avoid the problem of null boundaries. This feature is also useful for generative words. Experimental results on GENIA corpus are promising: nearly half of the possible terms were correctly recognized as a meaningful segment, and most of the remainin... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117958 Sat, 01 Jan 2005 07:00:00 +0100 117958 http://www.medworm.com/index.php?rid=117957&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972008%26dopt%3DAbstract Authors: Voit EO, Marino S, Lall R Modern methods of high-throughput molecular biology render it possible to generate time series of metabolite concentrations and the expression of genes and proteins in vivo. These time profiles contain valuable information about the structure and dynamics of the underlying biological system. This information is implicit and its extraction is a challenging but ultimately very rewarding task for the mathematical modeler. Using a well-suited modeling framework, such as Biochemical Systems Theory (BST), it is possible to formulate the extraction of information as an inverse problem that in principle may be solved with a genetic algorithm or nonlinear regression. However, two types of issues associated with this inverse problem make the extraction task dif... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117957 Sat, 01 Jan 2005 07:00:00 +0100 117957 http://www.medworm.com/index.php?rid=117956&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972009%26dopt%3DAbstract Authors: Borisjuk L, Hajirezaei MR, Klukas C, Rolletschek H, Schreiber F Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Webs... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117956 Sat, 01 Jan 2005 07:00:00 +0100 117956 http://www.medworm.com/index.php?rid=117955&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972010%26dopt%3DAbstract Authors: Dandekar T, Schmidt S Flexibility of metabolites and enzymes is investigated (i) on the level of the individual molecule, (ii) on the pathway level and (iii) combined effects on the systems and network level. Tools and results from our current research are summarized including data from our metabolite enzyme database. Including our latest census we find frequently used metabolites stimulate evolutionary flexibility in specific enzyme superfamilies. Furthermore, simultaneous changes of reactions and metabolites are observed in these flexible enzyme superfamilies. Both effects provide a strong source for resistance in parasites and pathogens. Specific adaptations scenarios and some counter strategies are discussed. PMID: 15972010 [PubMed - indexed for MEDLINE] (Source: In Si... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117955 Sat, 01 Jan 2005 07:00:00 +0100 117955 http://www.medworm.com/index.php?rid=117954&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972011%26dopt%3DAbstract Authors: Wishart DS, Yang R, Arndt D, Tang P, Cruz J A wide variety of approaches, ranging from Petri nets to systems of partial differential equations, have been used to model very specific aspects of cellular or biochemical functions. Here we describe how an agent-based or dynamic cellular automata (DCA) approach can be used as a very simple, yet very general method to model many different kinds of cellular or biochemical processes. Specifically, using simple pairwise interaction rules coupled with random object moves to simulate Brownian motion, we show how the DCA approach can be used to easily and accurately model diffusion, viscous drag, enzyme rate processes, metabolism (the Kreb's cycle), and complex genetic circuits (the repressilator). We also demonstrate how DCA approaches a... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117954 Sat, 01 Jan 2005 07:00:00 +0100 117954 http://www.medworm.com/index.php?rid=117953&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972012%26dopt%3DAbstract Authors: Broderick G, Ru'aini M, Chan E, Ellison MJ A framework is presented that captures the discrete and probabilistic nature of molecular transport and reaction kinetics found in a living cell as well as formally representing the spatial distribution of these phenomena. This particle or agent-based approach is computationally robust and complements established methods. Namely it provides a higher level of spatial resolution than formulations based on ordinary differential equations (ODE) while offering significant advantages in computational efficiency over molecular dynamics (MD). Using this framework, a model cell membrane has been constructed with discrete particle agents that respond to local component interactions that resemble flocking or herding behavioural cues in animals. ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117953 Sat, 01 Jan 2005 07:00:00 +0100 117953 http://www.medworm.com/index.php?rid=117952&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972013%26dopt%3DAbstract Authors: Pruess M, Kersey P, Apweiler R Integr8 (http://www.ebi.ac.uk/integr8/) is providing an integration layer for the exploitation of genomic and proteomic data by drawing on databases maintained at major bioinformatics centres in Europe. Main aims are to store the relationships of biological entities to each other and to entries in other databases, to provide a framework that allows for new kinds of data to be integrated, and to offer an entity-centric view of complete genomes and proteomes. Basic tools for data integration comprise the Proteome Analysis database, the International Protein Index (IPI), the Universal Protein sequence archive (UniParc) and the Genome Reviews. Entry points for the Integr8 portal depend on the users entity of interest: from browsing the taxonomy or wi... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117952 Sat, 01 Jan 2005 07:00:00 +0100 117952 http://www.medworm.com/index.php?rid=117951&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972014%26dopt%3DAbstract Authors: Turinsky AL, Ah-Seng AC, Gordon PM, Stromer JN, Taschuk ML, Xu EW, Sensen CW We have created a new Java-based integrated computational environment for the exploration of genomic data, called Bluejay. The system is capable of using almost any XML file related to genomic data. Non-XML data sources can be accessed via a proxy server. Bluejay has several features, which are new to Bioinformatics, including an unlimited semantic zoom capability, coupled with Scalable Vector Graphics (SVG) outputs; an implementation of the XLink standard, which features access to MAGPIE Genecards as well as any BioMOBY service accessible over the Internet; and the integration of gene chip analysis tools with the functional assignments. The system can be used as a signed web applet, Web Start, and a ... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117951 Sat, 01 Jan 2005 07:00:00 +0100 117951 http://www.medworm.com/index.php?rid=117950&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972015%26dopt%3DAbstract Authors: Fattore M, Arrigo P The possibility to study an organism in terms of system theory has been proposed in the past, but only the advancement of molecular biology techniques allow us to investigate the dynamical properties of a biological system in a more quantitative and rational way than before . These new techniques can gave only the basic level view of an organisms functionality. The comprehension of its dynamical behaviour depends on the possibility to perform a multiple level analysis. Functional genomics has stimulated the interest in the investigation the dynamical behaviour of an organism as a whole. These activities are commonly known as System Biology, and its interests ranges from molecules to organs. One of the more promising applications is the 'disease modeling'. T... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117950 Sat, 01 Jan 2005 07:00:00 +0100 117950 http://www.medworm.com/index.php?rid=117949&cid=s_32696_62_f&fid=32696&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15972016%26dopt%3DAbstract Authors: Chen M, Hofestaedt R Metabolic pathway alignment represents one of the most powerful tools for comparative analysis of metabolism. It involves recognition of metabolites common to a set of functionally-related metabolic pathways, interpretation of biological evolution processes and determination of alternative metabolic pathways. Moreover, it is of assistance in function prediction and metabolism modeling. Although research on genomic sequence alignment is extensive, the problem of aligning metabolic pathways has received less attention. We are motivated to develop an algorithm of metabolic pathway alignment to reveal the similarities between metabolic pathways. A new definition of the metabolic pathway is introduced. The algorithm has been implemented into the PathAligner sys... In Silico Biol journals http://www.medworm.com/rss/comments.php?id=117949 Sat, 01 Jan 2005 07:00:00 +0100 117949