http://www.bioinformatics.ca/links_directory/journals/nar/2010http://www.bioinformatics.ca/links_directory/journals/nar/2010/feed en http://www.sbg.bio.ic.ac.uk/3dligandsite3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.9208Wed, 16 May 2012 01:00:24 -0400 http://3vee.molmovdb.orgThe 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.9213Mon, 14 May 2012 18:30:04 -0400 http://bioinfo.cau.edu.cn/agriGO/agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.9219Wed, 16 May 2012 02:20:14 -0400 http://aladyn.escience-lab.orgThe ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.9220Mon, 14 May 2012 02:30:11 -0400 http://www.altanalyze.orgAltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).9225Thu, 17 May 2012 00:50:08 -0400 http://sing.ei.uvigo.es/ALTER/ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.9226Wed, 16 May 2012 23:40:10 -0400 http://structure.pitt.edu/anchorANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.10694Wed, 16 May 2012 04:10:06 -0400 http://www.babelomics.orgBabelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.9257Wed, 16 May 2012 07:00:05 -0400 http://bagel2.molgenrug.nlBAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.9258Tue, 15 May 2012 18:40:10 -0400 http://www.biocatalogue.org/A universal catalogue of web services for the life sciences. BioCatalogue provides a common interface for registering, browsing and annotating web services to the life science community.11329Tue, 15 May 2012 01:10:04 -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://www.sysbio.se/BioMetThe BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.9283Wed, 16 May 2012 00:10:10 -0400 http://www.beespace.uiuc.edu/QuestionAnswerBeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.10717Tue, 15 May 2012 15:30:03 -0400 http://mips.helmholtz-muenchen.de/proj/ccancerCCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.9330Wed, 16 May 2012 18:40:07 -0400 http://ccrxp.netasa.orgA tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.9331Wed, 16 May 2012 22:50:04 -0400 http://chipd.uwbacter.orgchipD is a web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage.9344Thu, 10 May 2012 23:10:13 -0400 http://gexp2.kaist.ac.kr/clicCLIC performs clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.9351Wed, 16 May 2012 09:00:06 -0400 http://sbi.postech.ac.kr/ConPlex/ConPlex is a web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structure.9369Wed, 16 May 2012 00:20:21 -0400 http://consurf.tau.ac.il/The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.9374Mon, 07 May 2012 16:30:04 -0400 http://www.cbs.dtu.dk/services/CPHmodels/CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling.9382Tue, 15 May 2012 07:10:09 -0400 http://cylofold.abcc.ncifcrf.gov/CyloFold is a web tool for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity.9393Wed, 16 May 2012 09:50:05 -0400 http://ekhidna.biocenter.helsinki.fi/dali_serverThe Dali server compares newly solved structures against structures in the PDB, allows browsing of pre-computed structural neighborhoods and generates suboptimal alignments from pairwise structure comparisons.9396Mon, 14 May 2012 10:10:06 -0400 http://120.107.8.16/dbcpThe Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.10705Wed, 16 May 2012 23:00:15 -0400 http://epsf.bmad.bii.a-star.edu.sg/struct_server.htmldeconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.9402Thu, 17 May 2012 01:00:39 -0400 http://dialign-tx.gobics.de/DIALIGN-TX is an update to DIALIGN. It combines the greedy heuristic method of DIALIGN with a traditional progressive method.9408Fri, 11 May 2012 12:50:13 -0400 http://www.prc.boun.edu.tr/appserv/prc/dnabindprotDNABINDPROT web tool is designed to predict DNA-binding residues in high frequency modes by the Gaussian network method.9421Wed, 16 May 2012 11:50:05 -0400 http://cpclab.uni-duesseldorf.de/dsppiDrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.10693Wed, 16 May 2012 22:20:15 -0400 http://dsap.cgu.edu.twDeep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are output based on homology mapping to Rfam and miRBase databases.10639Tue, 15 May 2012 02:30:05 -0400 http://bioinfo.ipmc.cnrs.fr/lea.htmle-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included.10648Mon, 14 May 2012 03:50:07 -0400 http://e-rnai.dkfz.de/E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.10049Sat, 12 May 2012 09:50:04 -0400 http://www.ebi.ac.uk/Tools/sssThe EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.10633Mon, 14 May 2012 23:00:06 -0400 http://www.embraceregistry.netEuropean Model for Bioinformatics Research and Community Education (EMBRACE) web service consists of EDAM, an ontology for describing life sciences; BioXSD, a schema for exchanging data between services and a centralized registry of ~1000 services.11326Wed, 16 May 2012 13:40:05 -0400 http://bioinfo3d.cs.tau.ac.il/FiberDock/FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function.10632Tue, 15 May 2012 17:20:10 -0400 http://salilab.org/foxsFast X-ray Scattering (FoXS) is a web server for computing the small angle x-ray scattering (SAXS) structure profile of a molecule in solution and for comparing the computed profile to the experimental profile.10673Tue, 15 May 2012 01:10:09 -0400 http://bioserv.rpbs.univ-paris-diderot.fr/fpocketFpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).10654Thu, 17 May 2012 00:40:07 -0400 http://rna.informatik.uni-freiburg.deThe Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.10638Wed, 16 May 2012 21:30:08 -0400 http://bioserv.rpbs.univ-paris-diderot.fr/Frog2Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.10653Tue, 15 May 2012 02:50:04 -0400 http://www.g-language.org/wiki/soap/G-language Genome Analysis Environment (G-language GAE) is a compendium of more than 100 programs that focus on bacterial genome analysis. Included are programs for identification of binding sites, analysis of codons and prediction of expression levels, analysis of nucleotide composition bias and visualization of genomic information.10624Tue, 15 May 2012 11:00:22 -0400 http://www.genemania.orgGeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.10715Wed, 16 May 2012 20:30:04 -0400 http://agknapp.chemie.fu-berlin.de/gplusGIS (Gangsta+ internet services) allows users to analyze protein structure families according to the SCOP classification scheme. Users can upload their own protein structures for pair-wise protein structure comparison, structure alignment or symmetry analysis.10634Wed, 16 May 2012 14:00:03 -0400 http://www.systemsbiology.org.au/glycoviewerThe GlycoViewer is a web-based tool that can visualize, summarize and compare sets of gylcan structures.10665Wed, 16 May 2012 12:40:11 -0400 http://grape.uwbacter.orgGRaphical Abstracted Protein Explorer (GRAPE) is a web server that allows users to explore abstracted representations of proteins. Large scale structural features are preserved while other surfaces are effectively reduced.10662Wed, 16 May 2012 13:40:13 -0400 http://gsa.muldas.orgGSA-SNP web server performs gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods.10686Fri, 11 May 2012 18:10:08 -0400 http://guidance.tau.ac.ilThe GUIDANCE web server assesses alignment confidence scores for the identification of unreliable alignment regions. Users input a set of unaligned sequences; output is a graphic visualization of the alignment with confidence scores at each residue.10656Wed, 16 May 2012 08:50:05 -0400 http://hexserver.loria.fr/A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.10623Tue, 15 May 2012 11:20:08 -0400 http://prism.ccbb.ku.edu.tr/hotpointHotPoint web server predicts hot spots in protein interfaces using an empirical model. Input is a protein complex and two chain identifiers that form an interface; output includes an interactive 3D visualization of the hot spots.10650Wed, 16 May 2012 16:10:12 -0400 http://gsea4gwas.psych.ac.cni-GSEA4GWAS is a web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS).10652Sun, 13 May 2012 00:50:10 -0400 http://bioinformatics.istge.it/ibws/The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa compiled a suite of free web services IBWS.11327Sat, 12 May 2012 14:30:07 -0400 http://dna.ccs.tulane.edu/icmThe Interactive Chromatin Modeling (ICM) web server is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates.10644Tue, 15 May 2012 20:10:05 -0400 http://gencomp.bio.unipd.it/magiamiRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data10672Wed, 16 May 2012 19:10:16 -0400 http://bioinformatics.zj.cn/magicviewer/MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.10641Sun, 13 May 2012 08:30:11 -0400 http://marq.dacya.ucm.esMARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.10680Thu, 17 May 2012 02:20:06 -0400 http://www.biokdd.fudan.edu.cn/Service/MetaMHC.htmlMetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.10688Tue, 15 May 2012 20:50:08 -0400 http://metexplore.toulouse.inra.frMetExplore is a web tool that links metabolites identified in untargeted metabolomics experiments within the context of genome-scale metabolic networks. Metabolomics data is mapped onto the specific metabolic network of an organism in a interactive graphical display.10631Wed, 16 May 2012 22:40:23 -0400 http://bioinfo-mml.sjtu.edu.cn/mGS/mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.10667Sun, 13 May 2012 19:50:05 -0400 http://centre.bioinformatics.zj.cn/mirtools/mirTools allows users to comprehensively characterize the small RNA transcriptome from high-throughput sequencing data. Users can filter quality reads, align short reads to the reference genome, classify small RNA candidates into known miRNAs, non-coding RNA, genomic repeats, etc. among other analysis tools.10678Thu, 17 May 2012 01:30:05 -0400 http://www.miru-vntrplus.orgMIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.10636Mon, 14 May 2012 19:20:11 -0400 http://www.inab.org/MOWServ/MOWServ provides integrated access to databases and analytical tools. Based on the BioMoby protocol for inter-service communication.10684Mon, 14 May 2012 15:00:07 -0400 http://proteinformatics.charite.de/mplot/MPlot is a web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.10671Thu, 17 May 2012 00:40:20 -0400 http://www.msea.caMetabolite Set Enrichment Analysis (MSEA) performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. MSEA uses a library of ~6300 predefined metabolite sets from pathways, disease signatures, genetic traits, and cellular/tissue locations. MSEA also facilitates conversion between metabolite common names, synonyms and other database identifies.10635Tue, 15 May 2012 10:20:06 -0400 http://MuD.tau.ac.ilMutation Detector (MuD) is a web server uses structural and sequence derived features to assess the impact of a given substitution on the protein function.9206Tue, 15 May 2012 19:20:10 -0400 http://www.ibi.vu.nl/programs/shmrwwwMulti-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.10677Wed, 16 May 2012 21:20:13 -0400 http://www.myexperiment.orgmyExperiment is an online research environment that supports the social sharing of bioinformatics workflows.11328Tue, 15 May 2012 14:30:15 -0400 http://proteomics.bioengr.uic.edu/NAPSNAPS is a web server for the prediction of specific residues involved in nucleic acid-binding proteins (NAPS) binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.10664Thu, 10 May 2012 06:30:09 -0400 http://molsim.sci.univr.it/constraintNMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom.10703Mon, 14 May 2012 21:10:15 -0400 http://www.ebi.ac.uk/olsThe Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain additional metadata and annotations. Improvements in 2010 have made OLS easier to use, capture more annotations from source data and integrate into external applications.10438Wed, 16 May 2012 22:00:08 -0400 http://ws.nbcr.netOpal Web Services for Biomedical Applications is a production web server. Powered by Opal, it allows users to use scientific applications easily as web services without any modification to the scientific codes.10713Wed, 16 May 2012 05:00:20 -0400 http://www.pandora.cs.huji.ac.ilThe PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides.10643Tue, 15 May 2012 05:30:13 -0400 http://www.ParticleStats.comParticleStats is a web server for particle motility analysis such as cytoskeleton. Input is X,Y coordinates of objects in time and output is novel analyses, graphical plots and statistics for motile objects.10700Wed, 16 May 2012 19:00:05 -0400 http://www.genome.jp/tools/pathpred/PathPred is an enzyme catalyzed metabolic pathway prediction server. Beginning with a query compound and chemical logic of enzymatic reactions (chemical structure transformation patterns of small molecules), biodegradation pathways of environmental compounds and biosynthesis pathways of secondary metabolites are predicted.10626Mon, 14 May 2012 20:30:13 -0400 http://pcfamily.life.nctu.edu.twThe PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.10669Wed, 16 May 2012 07:20:06 -0400 http://pcrtiler.alaingervais.org:8080/PCRTilerPCRTiler web server tool allows for the automated design of tiled primer pairs for any number of genomic loci. Based on Primer3 and BLAST analysis for cross-hybridization.10704Wed, 16 May 2012 01:20:05 -0400 http://www.peace-tools.orgParallel Environment for Assembly and Clustering of Gene Expression (PEACE) web tool performs high-throughput ab initio clustering of transcript fragment sequences from next-generation sequencing platforms.10691Sun, 13 May 2012 09:50:09 -0400 http://59.78.96.61/pharmmapperPharmMapper is a web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a given molecule to interact with a target.10622Wed, 16 May 2012 04:10:05 -0400 http://phenome.cchmc.orgPhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes.10708Sun, 13 May 2012 16:50:11 -0400 http://bayesweb.wadsworth.org/phyloscan/Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.10637Tue, 15 May 2012 11:40:06 -0400 http://csb2.ym.edu.tw/pint/Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.10699Wed, 16 May 2012 10:00:07 -0400 http://www.bioinformatics.sussex.ac.uk/PIRANHAThe PiRaNhA web server predicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.10676Tue, 15 May 2012 20:30:06 -0400 http://plastrna.njit.eduPLAST-ncRNA is an online tool for aligning distantly similar non-coding RNA sequences to a genome using the Probalign program. Useful for detection of potential homologous ncRNA sequences in large genomes.10707Mon, 14 May 2012 07:20:07 -0400 http://polyview.cchmc.org/conform.htmlPOLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.10660Wed, 16 May 2012 16:10:04 -0400 http://probis.cmm.ki.siProtein Binding Sites (ProBiS) is a web server which detects protein binding sites based on local structural alignments.10710Mon, 14 May 2012 10:00:08 -0400 http://www.prosess.caPROSESS (PROtein Structure Evaluation Suite and Server) is a comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling.10658Fri, 11 May 2012 16:30:08 -0400 http://proteindbs.rnet.missouri.edu/ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.9875Mon, 14 May 2012 10:50:08 -0400 http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGEPUDGE is a protein structure prediction server. Modeling is divided into 5 stages: template selection, alignment, model building, model refinement and model evaluation.10679Wed, 16 May 2012 12:10:16 -0400 http://mips.helmholtz-muenchen.de/proj/rspiderR spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome.10702Wed, 16 May 2012 00:50:09 -0400 http://regpredict.lbl.govRegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.10695Tue, 15 May 2012 17:50:04 -0400 http://kortemmelab.ucsf.edu/backrubThe RosettaBackrub server computes near-native conformational ensembles from a single input protein structure in PDB format using the Backrub method.10647Wed, 16 May 2012 13:50:22 -0400 http://galaxy.fml.mpg.derQuant.web is a web service for quantitative analysis of RNA sequencing data based on quadratic programming. rQuant.web is available as a tool in Galaxy.10696Tue, 15 May 2012 06:50:04 -0400 http://www.itb.cnr.it/rssRSSsite consists of a reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.10674Wed, 16 May 2012 03:40:04 -0400 http://phylogenomics.berkeley.edu/satchmo-jsSATCHMO-JS is a web server for simultaneous estimation of protein multiple sequence alignments and phylogenetic trees. Input is a FASTA file of sequences, and output is a phylogenetic tree and multiple sequence alignment.10646Sat, 12 May 2012 06:30:11 -0400 http://www.nii.ac.in/sbspks.htmlSBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.10628Mon, 14 May 2012 07:00:06 -0400 http://sea.bioinfo.cipf.esSerial Expression Analysis (SEA) suite of tools provides a complete resource for the analysis of serial transcriptomic data.10709Wed, 16 May 2012 12:50:08 -0400 http://selox.mpi-cbg.de/cgi-bin/selox/indexSeLOX web server identifies degenerate lox-like sites within genomic sequences.10712Wed, 16 May 2012 21:40:09 -0400 http://bioinf.cs.ucl.ac.uk/web_servers/A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.10019Thu, 10 May 2012 03:30:08 -0400 http://sfmap.technion.ac.ilSFmap is a web server for predicting putative splicing factor (SF) binding sites in genomic data. Sequences are input in FASTA format.10657Tue, 15 May 2012 03:10:13 -0400 http://www.genome.jp/tools/simcomp/SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.10642Wed, 16 May 2012 21:00:35 -0400 http://simfam.life.nctu.edu.tw/The SiMMap server statistically derives site-moiety maps which describe the relationship between moiety preferences and the physico-chemical properties of the binding site. Users input the interaction profiles of a query target protein and its docked compound.10663Tue, 15 May 2012 14:50:07 -0400 http://ccbg.imppc.org/sires/index.htmlSIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.10630Wed, 16 May 2012 20:50:12 -0400 http://bioware.ucd.ie/slimfinder.htmlSLiMFinder web server is a de novo motif discovery tool for short linear motifs (SLiMs). Statistically over represented motifs within a set of protein sequences are identified and scored. Users have numerous masking options to control the contextual information to be analyzed.10649Wed, 16 May 2012 10:10:04 -0400 http://kryptonite.ucsd.edu/opal2/GetServicesList.doThe SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.10670Wed, 16 May 2012 10:50:05 -0400 http://smog.ucsd.eduSMOG@ctbp is a web server for structure based modeling. It is based on the GROMACS molecular dynamics package and comes with tutorials.10687Mon, 14 May 2012 06:10:08 -0400 http://www.sequenceontology.org/cgi-bin/soba.cgiSequence Ontology Bioinformatics Analysis (SOBA) provides a simple statistical and graphical summary of an annotated genome. To be used by annotators and for genome comparison.10645Wed, 16 May 2012 02:10:05 -0400 http://speed.sys-bio.net/Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.10675Sat, 12 May 2012 08:40:10 -0400 http://spot.cgsmd.isi.eduThe SNP Prioritization Online Tool (SPOT) is a web server for integrating biological databases into the prioritization of SNPs for further study after a genome wide association study.10701Thu, 17 May 2012 00:30:16 -0400 http://struct2net.csail.mit.eduStruct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure based approach.10711Wed, 16 May 2012 16:50:04 -0400 http://targetfinder.org/Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.10685Wed, 16 May 2012 23:30:26 -0400 http://bioinfo.lifl.fr/TFMTFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.9296Wed, 16 May 2012 14:10:10 -0400 http://cbr.jic.ac.uk/threadmapperTHREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.10659Mon, 14 May 2012 21:10:04 -0400 http://togows.dbcls.jp/TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.9294Fri, 11 May 2012 03:30:09 -0400 http://toppcluster.cchmc.orgToppCluster is a human/mammalian genomes-centered web server application for comparative enrichment and network analysis of multiple gene lists. Features such as Gene Ontology terms, protein interactions,disease or disease-associated mammalian phenotypes, promoter cis-elements, miR binding sites, etc. that are differentially represented in the gene lists can be clustered or transformed into high dimensional Cytoscape or Gephi -compatible networks.10692Sat, 12 May 2012 06:10:08 -0400 http://transfind.sys-bio.net/TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets.10682Mon, 14 May 2012 13:50:10 -0400 http://translatorx.co.ukTranslatorX is a web-server designed to align protein coding nucleotide sequences based on their corresponding amino acid translations rather than nucleotide alignments.10627Wed, 16 May 2012 02:00:07 -0400 http://visibioweb.patika.orgVISIBIOweb is a web-based pathway visualization and layout service for pathway models in BioPAX format. Models are based on the Systems Biology Graphical Notation and pathway object properties such as external database references, may be inspected interactively.10640Tue, 15 May 2012 07:40:09 -0400 http://wavi.bioinfo.cnio.eswaviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.10690Wed, 16 May 2012 21:20:22 -0400 http://webprinses.epfl.ch/WebPrInSeS is a web server that allows automated full-length clone sequence identification and verification using high-throughput sequencing data from any of the 3 major sequencing platforms.10661Wed, 16 May 2012 16:50:12 -0400 http://swift.cmbi.ru.nl/WHAT IF Web Services (WIWS) is a web service based on the WHAT IF software package for macromolecular analysis, visualization, modeling and structure validation. This protein structure bioinformatics web service collection has over 1600 different functions.10666Wed, 16 May 2012 16:30:08 -0400 http://www.multiloc.org/YLocYLoc is a web server for the prediction of subcellular localization. Predictions are explained and biological properties used for the prediction highlighted. In addition, a confidence estimates rates the reliability of individual predictions. 10683Thu, 10 May 2012 23:50:12 -0400 http://bindr.gdcb.iastate.edu/ZiFiT/ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.10346Wed, 16 May 2012 17:30:09 -0400