http://www.bioinformatics.ca/links_directory/journals/nar/2009http://www.bioinformatics.ca/links_directory/journals/nar/2009/feed en http://haddock.chem.uu.nl/dna/The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.9204Tue, 15 May 2012 05:20:12 -0400 http://abcis.cbs.cnrs.fr/AT2/@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.9214Tue, 15 May 2012 07:40:07 -0400 http://annie.bii.a-star.edu.sgANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.9232Mon, 14 May 2012 03:10:07 -0400 http://influenza.nhri.org.tw/ATIVS/ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.9253Tue, 15 May 2012 13:30:05 -0400 http://www.ijm.fr/en/ijm/resources/bioinformatics/AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.10571Thu, 17 May 2012 01:50:07 -0400 http://www.Biobike.orgBioBIKE is a web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. BioBIKE is composed of three components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Users may also invent their own tools.9271Tue, 08 May 2012 07:30:06 -0400 http://www.bioinformatics.ca/links_directory/The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.11303Mon, 07 May 2012 01:10:05 -0400 http://biomart.orgBioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).9282Wed, 16 May 2012 05:50:17 -0400 http://bioportal.bioontology.orgBioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.9288Wed, 16 May 2012 17:40:13 -0400 http://www.ncrna.org/centroidfold/Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).9337Thu, 17 May 2012 01:50:06 -0400 http://www.clantox.cs.huji.ac.ilClanTox, a classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.9350Tue, 15 May 2012 14:30:05 -0400 http://prodata.swmed.edu/compass/compass.phpCOMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.9368Tue, 15 May 2012 19:00:07 -0400 http://cops.services.came.sbg.ac.at/The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.9376Wed, 16 May 2012 02:20:14 -0400 http://tlife.fudan.edu.cn/cvtreeComposition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.9392Wed, 16 May 2012 15:30:04 -0400 http://www.biotec.or.th/isl/DomixA Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.9395Wed, 16 May 2012 10:10:13 -0400 http://www.dasmiweb.deThe DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.9397Wed, 16 May 2012 23:30:27 -0400 http://www.microrna.gr/microTThe DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.9409Thu, 17 May 2012 00:20:13 -0400 http://www.ebi.ac.uk/Tools/webservices/EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.10038Mon, 14 May 2012 21:30:05 -0400 http://FMM.mbc.nctu.edu.tw/From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.10599Tue, 15 May 2012 23:50:10 -0400 http://bioinformatics.clemson.edu/G-SESAMEG-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.10580Tue, 15 May 2012 09:30:08 -0400 http://gendoo.dbcls.jpGene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.10577Tue, 15 May 2012 08:10:10 -0400 http://genecodis.dacya.ucm.esOriginally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.10570Sun, 13 May 2012 13:00:10 -0400 http://mips.helmholtz-muenchen.de/proj/gene2mir/GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.9295Wed, 16 May 2012 07:40:06 -0400 http://www.genmr.caGenerate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.10563Tue, 15 May 2012 07:00:09 -0400 http://www.genocad.orgGenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.10610Tue, 15 May 2012 05:40:14 -0400 http://bioinfo.cipf.es/gesbap/Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.10589Tue, 15 May 2012 21:10:36 -0400 http://gopubmed.biotec.tu-dresden.de/gogeneGoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.10541Tue, 15 May 2012 09:30:05 -0400 http://toolkit.tuebingen.mpg.de/hhompHHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.10546Fri, 11 May 2012 19:20:08 -0400 http://biodb.jp/The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using the corresponding tables in HMS.9304Mon, 14 May 2012 22:00:06 -0400 http://www.homozygositymapper.orgA web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.10557Wed, 16 May 2012 07:10:05 -0400 http://prodata.swmed.edu/horaserver/HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.10566Wed, 16 May 2012 03:00:04 -0400 http://loschmidt.chemi.muni.cz/hotspotwizard/HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.10600Tue, 15 May 2012 16:20:05 -0400 http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jspA web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.10560Mon, 14 May 2012 09:50:10 -0400 http://insignia.cbcb.umd.eduInsignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.10536Wed, 16 May 2012 01:30:05 -0400 http://phylogenomics.berkeley.edu/intrepidThe INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.10597Tue, 15 May 2012 05:10:15 -0400 http://sarst.life.nthu.edu.tw/iSARST/iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.10604Fri, 11 May 2012 18:30:06 -0400 http://jphmm.gobics.de/Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.10257Mon, 14 May 2012 13:10:06 -0400 http://www.litinspector.org/A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.10543Wed, 16 May 2012 19:00:13 -0400 http://ms.iis.sinica.edu.tw/MaXIC-QThe MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.10579Tue, 15 May 2012 17:10:04 -0400 http://cbdm.mdc-berlin.de/tools/medlinerankerThe MedlineRanker web server allows a flexible and fast ranking of Medline abstracts for a topic of interest without expert knowledge. 10551Mon, 14 May 2012 12:50:08 -0400 http://meme.nbcr.net/meme/intro.htmlThe MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.10615Wed, 16 May 2012 18:30:04 -0400 http://www.metaboanalyst.caMetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis. 10562Mon, 14 May 2012 13:20:08 -0400 http://www.mgene.org/webmGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.10587Wed, 16 May 2012 07:40:21 -0400 http://mgip.biology.gatech.eduThe Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.10549Wed, 16 May 2012 17:10:04 -0400 http://microbe.vital-it.chThe Microbe Browser is a web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5 software packages is also displayed.10531Wed, 16 May 2012 05:00:22 -0400 http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.10593Wed, 16 May 2012 18:10:04 -0400 http://www.mirz.unibas.chMirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.10582Tue, 15 May 2012 20:10:07 -0400 http://cancer.informatics.indiana.edu/mmiamicroRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).10607Wed, 16 May 2012 23:50:11 -0400 http://bcb.dei.unipd.it/MolLocMolecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.10592Wed, 16 May 2012 10:20:11 -0400 http://cssp2.sookmyung.ac.krA web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.10529Wed, 16 May 2012 15:50:06 -0400 http://casp.rnet.missouri.edu/nncon.htmlUsing 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.10548Mon, 14 May 2012 13:40:11 -0400 http://sourceforge.net/projects/omicbrowse/OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset.10612Thu, 17 May 2012 02:10:11 -0400 http://www.epitoolkit.org/optitopeOpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolKit.10591Wed, 16 May 2012 16:30:13 -0400 http://orphelia.gobics.deOrphelia is a machine learning program for predicting genes in short DNA sequences from metagenomic sequencing projects. The program encompasses fragment length specific prediction models for chain termination sequencing and pyrosequencing.10564Thu, 17 May 2012 02:30:14 -0400 http://orthoselect.gobics.deOrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.10576Wed, 16 May 2012 17:50:09 -0400 http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.10358Sat, 12 May 2012 02:40:06 -0400 http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLDPEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution.10542Thu, 17 May 2012 00:00:18 -0400 http://phemto.orgchm.bas.bg/Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.10258Tue, 15 May 2012 19:20:05 -0400 http://phylofacts.berkeley.edu/orthologs/The PHOG web server identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds.10583Tue, 15 May 2012 00:10:04 -0400 http://www.ibi.vu.nl/programs/phylopars/The PhyloPars web server allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.10558Tue, 15 May 2012 08:50:16 -0400 http://zope.bioinfo.cnio.es/plan2lA web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.10588Wed, 16 May 2012 21:50:17 -0400 http://www.nipgr.res.in/plecdom.htmlPLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.10578Thu, 10 May 2012 23:50:15 -0400 http://pomelo2.bioinfo.cnio.esPomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.10532Thu, 17 May 2012 03:10:07 -0400 http://omicspace.riken.jp/PosMed/To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.10550Sat, 12 May 2012 08:20:08 -0400 http://gemdock.life.nctu.edu.tw/ppisearch/PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.10608Tue, 15 May 2012 17:40:05 -0400 http://prep.unl.edu/The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.10567Wed, 16 May 2012 16:50:07 -0400 http://maya.ccg.unam.mx/primers4clades/Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein coding genes, primers4clades aligns the sequences, computes a neighbor-joining tree and designs lineage specific primers for the user selected species or sequence clusters.10554Tue, 15 May 2012 19:00:04 -0400 http://www.bioinformatics.nl/progmapProtein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.10572Thu, 17 May 2012 01:40:07 -0400 http://prodata.swmed.edu/ProSMoS/ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.10598Sun, 06 May 2012 03:10:04 -0400 http://protedna.csbb.ntu.edu.tw/ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.10585Wed, 16 May 2012 16:30:10 -0400 http://xtal.nki.nl/ccdProtein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.10613Wed, 16 May 2012 06:20:05 -0400 http://protinfo.compbio.washington.edu/ppc/Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.10555Wed, 16 May 2012 04:20:03 -0400 http://www.beaconlab.it/pscanPscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.10584Tue, 15 May 2012 17:40:10 -0400 http://pubchem.ncbi.nlm.nih.gov/assay/PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.10611Sat, 12 May 2012 04:30:11 -0400 http://swissmodel.expasy.org/qmeanQMEAN is a web server for protein model quality estimation. Either the composite scoring function QMEAN or the clustering based scoring function QMEANclust may be used.10538Tue, 15 May 2012 20:10:06 -0400 http://biodev.extra.cea.fr/rasmot3d/The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology.10544Wed, 16 May 2012 18:00:05 -0400 http://www.nii.ac.in/~deepak/RegAnalyst/RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).10559Mon, 14 May 2012 13:40:10 -0400 http://proteinformatics.charite.de/rhythm/RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.10605Tue, 15 May 2012 09:30:07 -0400 http://bioinformatics.bc.edu/clotelab/RNAmutants/A web server to explore the effect of mutations on the RNA secondary structures.10581Tue, 15 May 2012 07:50:05 -0400 http://antibody.graylab.jhu.eduThe RosettaAntibody server predicts the structure of an antibody variable region given the amino acid sequences of the light and heavy chains. 2000 independent structures are generated and scored, with the top 10 models being returned in high resolution and detailed format.10530Tue, 15 May 2012 17:20:06 -0400 http://www.zbh.uni-hamburg.de/salamiThe SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity and sequence alignments.10573Thu, 17 May 2012 00:40:03 -0400 http://sgu.bioinfo.cipf.es/services/SARA/Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function. The server can also be used for RNA pairwise structure alignment. 10575Mon, 14 May 2012 19:30:07 -0400 http://seemotif.csie.ntu.edu.twThe web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).10586Mon, 14 May 2012 20:20:05 -0400 http://sent.dacya.ucm.esSENT is a text mining web server. SENT uses non-negative matrix factorization to identify topics in scientific articles associated with an input list of genes.10553Wed, 16 May 2012 11:20:07 -0400 http://lifecenter.sgst.cn/seppa/index.phpA computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA) based on a 'unit patch of residue triangle' description of local spatial context in protein surface.10574Tue, 15 May 2012 20:50:05 -0400 http://SePreSA.Bio-X.cn/SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.10534Thu, 17 May 2012 01:00:34 -0400 http://sib-blast.osc.eduSIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.10533Tue, 15 May 2012 08:00:13 -0400 http://sitehound.sanchezlab.orgSITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.10595Wed, 16 May 2012 17:00:12 -0400 http://bioinfo.mc.ntu.edu.tw/slither/SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.10609Wed, 16 May 2012 09:40:05 -0400 http://snow.bioinfo.cipf.esSNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance estimates.10528Tue, 15 May 2012 00:40:06 -0400 http://www.niehs.nih.gov/snpinfoA suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.10565Tue, 15 May 2012 05:30:06 -0400 http://pocket.uchicago.edu/SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.10602Mon, 14 May 2012 05:00:06 -0400 http://sroogle.tau.ac.ilSROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.10535Wed, 16 May 2012 01:10:11 -0400 http://bioinf-applied.charite.de/superlooper/SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.10601Wed, 16 May 2012 17:00:06 -0400 http://prime.ibn.a-star.edu.sgTmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.10561Wed, 16 May 2012 14:30:26 -0400 http://topcons.netTOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.10614Wed, 16 May 2012 15:00:18 -0400 http://toppgene.cchmc.orgToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.10569Tue, 15 May 2012 07:30:04 -0400 http://www.cs.tau.ac.il/~bnet/torque.htmlTorque is a web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.10568Fri, 11 May 2012 10:20:09 -0400 http://uniprime.batlab.euThe UniPrime2 web server designs large sets of universal primers when provided with a gene reference ID or FASTA sequence. UniPrime2 works by integrating Blastn, T-Coffee, GramAlign and Primer3 into a single software pipeline.10552Tue, 15 May 2012 21:40:05 -0400 http://bioafrica.mrc.ac.za/rega-genotype/html/This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.10590Tue, 15 May 2012 23:20:07 -0400 http://visant.bu.edu/VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.10070Wed, 16 May 2012 03:20:08 -0400 http://biit.cs.ut.ee/vishicVisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.10606Tue, 15 May 2012 20:30:04 -0400 http://w3dna.rutgers.eduThe web 3DNA server is the web interface for the 3DNA suite of programs developed for the analysis, reconstruction and visualization of 3D nucleic acid containing structures.10596Sat, 12 May 2012 14:50:04 -0400 http://www.bioinfolab.org/software/webgmapA web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.10594Sun, 13 May 2012 16:10:05 -0400 http://weblab.cbi.pku.edu.cnAn integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share data under an intuitive web interface. These tools can be further organized as customized workflows.10540Wed, 16 May 2012 11:40:15 -0400 http://www.ibi.vu.nl/programs/prcwww/Web Profile Comparer (webPRC) is a web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An alignment editor allows for user editing of output alignments.10547Mon, 14 May 2012 13:00:13 -0400 http://www.whichgenes.org/WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers.10539Mon, 14 May 2012 13:40:12 -0400 http://bioserv.rpbs.univ-paris-diderot.fr/wwLigCSRre.htmlThe wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.10545Wed, 16 May 2012 09:40:06 -0400