http://www.bioinformatics.ca/links_directory/journals/nar/2008http://www.bioinformatics.ca/links_directory/journals/nar/2008/feed en http://3dfun.bioinfo.pl3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.9205Wed, 16 May 2012 14:50:06 -0400 http://bioalgo.iit.cnr.it/amicaThe All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.9229Wed, 16 May 2012 18:10:05 -0400 http://sysbio.kribb.re.kr/AsiDesigner/AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.9246Tue, 15 May 2012 04:40:07 -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://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://biolit.ucsd.eduBioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontology terms.9281Mon, 14 May 2012 18:40:11 -0400 http://bionmf.dacya.ucm.es/A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.10430Wed, 16 May 2012 04:00:04 -0400 http://www.ncbi.nlm.nih.gov/BLAST/Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.9622Tue, 15 May 2012 06:50:07 -0400 http://stothard.afns.ualberta.ca/cgview_server/The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.9338Tue, 15 May 2012 19:20:06 -0400 http://bioit.dmbr.ugent.be/ConTra/index.phpThe Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web server allows users to interactively visualize transcription factor binding sites predicted using TransFac, JASPAR or PWM libraries on aligned promoter sequences. Nine reference organisms are supported for analysis of promoter regions, 5' UTRs, 3' UTRs and introns.9375Sat, 12 May 2012 16:20:04 -0400 http://www.copub.orgCoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.9377Mon, 14 May 2012 21:00:13 -0400 https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.htmlThe Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.9380Wed, 16 May 2012 09:10:05 -0400 http://crispr.u-psud.fr/CRISPRcompar/Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.9384Thu, 17 May 2012 00:50:05 -0400 http://www.cs23d.caChemical Shift to 3D Structure (CS23D) generates accurate 3D protein structures using only NMR chemical shifts and sequence data. Output is a set of PDB coordinates for the protein.9389Sun, 13 May 2012 16:00:21 -0400 http://sitron.bccs.uib.no/dhcl/DHcL provides analysis of the hierarchy of protein domain structures. DHcL detects closed loops and van der Waals locks, and outputs domain decomposition at different levels of protein domain structure hierarchy.10431Tue, 15 May 2012 03:20:06 -0400 http://dire.dcode.orgA web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.9415Fri, 11 May 2012 12:30:14 -0400 http://e1ds.ee.ncku.edu.tw/E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.10453Wed, 16 May 2012 02:50:04 -0400 http://e3miner.biopathway.orgE3Miner is a web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published literature as well as from the biological databases.10479Sat, 05 May 2012 21:00:07 -0400 http://www.esat.kuleuven.be/endeavourENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.12956Sun, 13 May 2012 15:10:06 -0400 http://www.epitoolkit.orgA suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.10437Mon, 14 May 2012 07:50:05 -0400 http://bioinf.cs.ucl.ac.uk/ffpred/Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.10436Sat, 12 May 2012 21:50:07 -0400 http://bioinfo3d.cs.tau.ac.il/FireDock/The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.10434Mon, 07 May 2012 21:50:06 -0400 http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.plThe Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.10432Tue, 15 May 2012 11:00:18 -0400 http://genecat.mpg.deThe Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.10442Sun, 13 May 2012 00:20:06 -0400 http://genepipe.ngc.sinica.edu.tw/genowatchA disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.10462Sun, 13 May 2012 22:10:11 -0400 http://www.gepas.orgThe Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.9917Wed, 16 May 2012 08:50:06 -0400 http://guinevere.otago.ac.nz/stats.htmlGLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.10083Tue, 15 May 2012 15:10:06 -0400 http://omicslab.genetics.ac.cn/GOEAST/Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.10498Wed, 16 May 2012 17:10:06 -0400 http://biit.cs.ut.ee/graphweb/GraphWeb is a web server for biological network analysis and module design using a graphical interface.10471Mon, 14 May 2012 11:20:05 -0400 http://hub.iis.sinica.edu.tw/HubbaHub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.10455Tue, 15 May 2012 02:30:06 -0400 http://www.idtdna.com/SciTools/SciTools.aspxIDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.10451Thu, 17 May 2012 01:30:07 -0400 http://tools.immuneepitope.orgThe Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools.10447Mon, 07 May 2012 06:10:03 -0400 http://imgt.cines.fr/The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.9847Tue, 15 May 2012 16:40:04 -0400 http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.plThe ISPIDER Central provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics.10433Tue, 15 May 2012 23:10:12 -0400 http://www.compbio.dundee.ac.uk/jpredJpred 3 is an improved web server for predicting protein secondary structure in three states (alpha helix, beta strand and coil). Improvements include better usability, batch submission of sequences and updates to the search databases.10440Wed, 16 May 2012 17:00:12 -0400 http://www.genome.ad.jp/kegg/Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.11391Sun, 13 May 2012 04:40:08 -0400 http://www.mitchell-lab.org/kfcThe KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.10469Tue, 15 May 2012 00:30:04 -0400 http://bioinformatics.bc.edu/clotelab/localmove/LocalMove is a web server for computing on-lattice fits for biopolymersusing input from PDB files for proteins or RNA molecules. Results are output in PDB file format and include a 3D movie of the intermediate conformations simulated during computation.10504Fri, 11 May 2012 13:00:04 -0400 http://www.bioinfo.hr/madnetMicroarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.10495Wed, 16 May 2012 22:30:06 -0400 http://bioinfo.lifl.fr/magnoliaMAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern.10476Wed, 16 May 2012 05:10:04 -0400 http://bioinfo3d.cs.tau.ac.il/MAPPISMultiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces.10487Tue, 15 May 2012 05:50:13 -0400 http://massnet.krMassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.10465Sat, 12 May 2012 05:50:12 -0400 http://masstrix.orgWith applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.10445Wed, 16 May 2012 03:00:09 -0400 http://www.lgtc.nl/MaRe/Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.10483Wed, 16 May 2012 12:40:08 -0400 http://mkt.uab.esStandard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.10502Thu, 17 May 2012 01:30:19 -0400 http://bioinfo3d.cs.tau.ac.il/MolAxisThe MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.10456Wed, 16 May 2012 03:50:05 -0400 http://bioinfo3d.cs.tau.ac.il/MultiBindMultiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.10486Fri, 11 May 2012 17:50:06 -0400 http://rsat.ulb.ac.be/neat/Network Analysis Tools (NeAT) is a suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.10499Wed, 16 May 2012 17:10:07 -0400 http://www.cbs.dtu.dk/services/NetMHCNetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.10452Mon, 14 May 2012 07:50:08 -0400 http://www.manet.uiuc.edu/nobai/nobai.phpNOBAI web server facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules.10463Wed, 16 May 2012 21:30:05 -0400 http://bioinfo.unice.fr/ohm/OligoHeatMap is an online tool for estimation of melting temperatures for sets of oligonucleotides and positioning of oligomers within sets of aligned sequences. Oligomer positioning on sequences is displayed graphically.10461Mon, 14 May 2012 15:20:11 -0400 http://rna.urmc.rochester.edu/servers/oligowalkOligoWalk is an online sever for designing efficient siRNA targeting a given mRNA sequence. By calculating thermodynamic features of sense-antisense hybidization, OligoWalk predicts the free energy changes of oligonucleotides binding to a target RNA.10470Sun, 13 May 2012 10:10:06 -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://mips.gsf.de/genre/proj/orest/index.htmlOnline Resource for EST (OREST) analysis is a EST analysis pipeline which allows rapid analysis of large amounts of ESTs or cDNAs from mammals and fungi. Functional annotation of the dataset is also included via either FunCat or GO annotation.10496Mon, 14 May 2012 13:00:14 -0400 http://pals.bioinfo.cnio.esPathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.10467Wed, 16 May 2012 06:40:05 -0400 http://www.charmm-gui.org/?doc=input/pbeqsolverPBEQ-Solver is a wb based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann equations and interactively display the eletrostatic potential.10500Tue, 15 May 2012 08:00:14 -0400 http://bioinfo3d.cs.tau.ac.il/PharmaGistPharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design.10444Tue, 15 May 2012 20:00:04 -0400 http://www.phylogeny.fr/Phylogeny.fr is a seamless automation of the various components in pylogenetic analyses from identification of homologous sequences, construction of multiple alignments, phylogenetic reconstruction to graphical representation of the inferred phylogenetic tree.10459Wed, 16 May 2012 09:10:06 -0400 http://bi.snu.ac.kr/pie/The Protein Interaction information Extraction system (PIE) is a configurable web server for extraction of protein-protein interactions from literature. Both co-occurrence of proteins in text and predefined phrase patterns for protein-protein interactions are employed in a machine learning framework.10448Sat, 12 May 2012 22:50:23 -0400 http://wishart.biology.ualberta.ca/polysearchPolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences.10480Mon, 07 May 2012 17:10:04 -0400 http://predikin.biosci.uq.edu.auThe Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation10492Wed, 16 May 2012 23:10:05 -0400 http://www.prodonet.tu-bs.deA web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.10473Sun, 13 May 2012 12:30:05 -0400 http://webclu.bio.wzw.tum.de/profcom/Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.10472Wed, 16 May 2012 10:20:18 -0400 http://prodata.swmed.edu/promals3dPROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.10401Sun, 13 May 2012 11:50:09 -0400 http://wishart.biology.ualberta.ca/proteus2PROTEUS2 is a web server for comprehensive protein structure prediction and structure-based annotation. The analysis pipeline includes signal identification, trans-membrane helix prediction, trans-membrane beta-strand prediction, secondary structure prediction and homology modeling for user inputs of single or multiple sequences.10468Wed, 16 May 2012 01:00:06 -0400 http://bioinfo3.noble.org/pssRNAMiner/pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.10493Wed, 16 May 2012 11:10:22 -0400 http://imed.med.ucm.es/PVS/Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments.10464Fri, 11 May 2012 17:30:07 -0400 http://quma.cdb.riken.jp/Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.10478Tue, 15 May 2012 08:50:09 -0400 http://www.tcoffee.orgThe R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures.10439Wed, 16 May 2012 20:10:06 -0400 http://webapps.embl-hamburg.de/rapidoRAPIDO conducts 3D alignments of crystal structures of different protein molecules in the presence of conformational change.10489Tue, 15 May 2012 12:00:11 -0400 http://rnalogo.mbc.nctu.edu.tw/RNALogo is a tool for graphical representation of features within multiple RNA sequence alignments and their consensus RNA secondary structures. Each RNA family in Rfam has been graphically evaluated for a logo.10491Mon, 14 May 2012 19:40:07 -0400 http://rosettadock.graylab.jhu.eduRosettaDock server is a structure prediction program that searches the rigid body and side chain conformational space of two interacting proteins to find a minimum free-energy complex for the protein-protein interaction structure.10450Tue, 15 May 2012 11:00:11 -0400 http://rsat.ccb.sickkids.ca/Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.10112Tue, 15 May 2012 21:20:05 -0400 http://www.compbio.dundee.ac.uk/www-scanpsSCANPS is a web server for iterative protein sequence database searching by dynamic programming. Sensitivity and selectivity outperform PSI-BLAST. The server allows a range of different protein sequence databases to be searched including the SCOP database of protein domains.10477Thu, 17 May 2012 02:20:09 -0400 http://www.bioinformatics.nl/tools/seqatomsSEQATOMS is a web tool for identifying missing regions in PDB sequence. To visualize these regions in their sequence context, a BLAST interface is used that is able to show the lower-case masked regions in the output (hits in the BLAST output are replaced with the corresponding subsequence from the original FASTA files).10474Sat, 12 May 2012 13:30:10 -0400 http://www.geneontology.org/GO.tools.microarray.shtmlSearching for the best GO tool (SerbGO) helps users select the GO annotation or list analysis tools which best suit their needs. SerbGO may also be used to compare the capabilities of the various GO tools in the context of the users' experiment.10454Tue, 08 May 2012 12:30:09 -0400 http://www.cmbi.ru.nl/signatureSignature identifies signature genes or genes that are unique to a taxonomic clade and thus useful in phylogenetic analysis. Users input a set of query sequences and returned is a list of taxonomic clades that share signatures with the query.10494Mon, 14 May 2012 07:50:10 -0400 http://soapdb.sourceforge.net/soaPDB is a web application for the generation and organization of saved PDB searches as well email notifications.10503Thu, 17 May 2012 01:40:06 -0400 http://software.ncrna.orgA suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.10488Tue, 15 May 2012 20:10:09 -0400 http://bioinformatics.charite.de/superimposeSuperimpose web server performs structural similarity searches for small molecules, parts of proteins (i.e. binding sites) or whole proteins, with a preference towards 3D structure based methods. Users are assisted in selection of algorithms and databases that best suit their needs.10497Wed, 16 May 2012 02:30:05 -0400 http://bioinformatics.charite.de/superpredThe SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction.10466Wed, 16 May 2012 10:30:17 -0400 http://snowwhite.wellesley.edu/targetRNATargetRNA is a web based tool for identifying mRNA targets of small non-coding RNAs in bacterial species.10449Wed, 16 May 2012 11:00:13 -0400 http://www.compbio.dundee.ac.uk/taroTarO is a collection of tools for protein target optimization analysis. Tools include those for annotation of putative orthologues and homologues, searches against the PDB with PSIBLAST, generation of annotated multiple sequence alignments and presentation of integrated results.10457Thu, 17 May 2012 02:40:08 -0400 http://umbbd.msi.umn.edu/predict/The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made.10485Fri, 11 May 2012 18:10:07 -0400 http://rna.tbi.univie.ac.at/Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. Tools include folding of single and aligned sequences, prediction of RNA-RNA interactions, design of sequences with a given structure, analysis of folding landscapes and structural RNA alignments using LocARNA.10460Thu, 10 May 2012 15:40:12 -0400 http://genome.ku.dk/resources/warWebserver for Aligning structural RNAs (WAR) is a collection of methods for performing multiple alignments and secondary structure prediction for non-coding RNA sequences. The methods can be run simultaneously and a consensus prediction calculated.10446Mon, 14 May 2012 02:20:09 -0400 http://pat.kobic.re.kr/wdac/index.htmThe WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.10458Wed, 16 May 2012 12:20:06 -0400 http://pipsa.h-its.orgwebPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The resulting matrices of pairwise electrostatic similarities may be visualized as epograms or heat maps.10435Tue, 15 May 2012 09:50:15 -0400 http://biowiki.org/XreiProgramxREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.10441Mon, 14 May 2012 01:30:06 -0400