GeoMineGeoMine enables the automated mining of protein-ligand binding sites. Based on individually designed queries, users can search for spatial interaction patterns in huge collections of protein-ligand complexes and binding pockets. The regularly updated GeoMine database relies on the free database systems SQLite and PostgreSQL. It supports radius-based pockets (based on ligands and predicted pockets (based on DoGSite3) for query generation. The query management is based on XML (for the REST service) or JSON in the GUI mode. Its output consists of the query-based superpositions of the matched binding sites and statistics on matching points, distances, and angles.https://www.zbh.uni-hamburg.de/forschung/amd/software/geomine.htmlgeominebiotools:geomineWeb serviceWeb APIhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3336Drug discoveryLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF

http://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1481Protein structure alignmenthttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1497Root-mean-square deviation

textual, numerical, and chemical 3D searches in the PDBhttps://proteins.plusServiceA web service to run GeoMine calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/geomine_restServiceA web API to run GeoMine calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/indexGeneraldogsite3usesprotossuses10.1093/bioinformatics/btaa69332735322Usage10.1021/acs.jcim.6b00561Method10.1021/acs.jmedchem.1c01046Primary10.1007/s10822-024-00563-3UsageProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderDISULFINDDISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.http://disulfind.dsi.unifi.it/disulfindbiotools:disulfindWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_1850Protein cysteine and disulfide bond assignmenthttp://edamontology.org/operation_3092Protein feature detectionhttp://disulfind.dsi.unifi.it/help.phpGeneral10.1093/nar/gkl26616844986PMC153882310.1093/bioinformatics/btg4631503387210.1093/nar/gkr36521576237PMC312577110.1093/bioinformatics/btn37118635571PMC2732205DISULFIND Supportdisulfind@ai.dinfo.unifi.itPersonPrimary contactFusionEncoderFusionEncoder is a web server and predictor for identifying intrinsically disordered regions (IDRs) in proteins by integrating traditional biological features and protein language models using a novel LSTM-based fusion network. It demonstrates improved accuracy compared to existing methods.http://bliulab.net/FusionEncoder/fusionencoderbiotools:fusionencoderhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3538Protein disordered structurehttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/operation_0470Protein secondary structure prediction (coils)http://edamontology.org/operation_3937Feature extractionhttp://edamontology.org/operation_3904Protein disorder predictionhttp://edamontology.org/operation_3891Essential dynamics10.1093/BIOINFORMATICS/BTAF36240577786PMC12231546Bin Liubliu@bliulab.nethttps://orcid.org/0000-0003-3685-9469PersonAggreProtAggreProt is a web server to predict and engineer protein aggregation. The tool provides a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.https://loschmidt.chemi.muni.cz/aggreprot/aggreprotbiotools:aggreprot1.0Web servicehttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavaJavaScriptProprietaryMatureFree of chargeOpen accessToolsProteomicsCzech Republic10.1093/nar/gkae420PrimaryJoan Planas-IglesiasDavid BednarJiri DamborskySimeon BorkoFolddiscoFolddisco enables rapid detection of discontinuous or segment 3D motifs in large protein databses.https://github.com/steineggerlab/folddiscofolddiscobiotools:folddiscoCommand-line toolWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0166Protein structural motifs and surfacesLinuxMacRustGPL-3.0EmergingFree of chargehttps://github.com/steineggerlab/folddisco/issuesIssue trackerhttps://search.foldseek.com/folddiscoService10.1101/2025.07.06.663357v1CleavPredictA Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events.http://cleavpredict.sanfordburnham.org/cleavpredictbiotools:cleavpredictWeb applicationhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_0250Protein property calculationhttp://cleavpredict.sanfordburnham.org/tutorialGeneral10.1371/JOURNAL.PONE.012787725996941PMC4440711Supportskumar@sanfordburnham.orgPersonPrimary contactSupportpcieplak@sanfordburnham.orgPersonPrimary contactSiteEngineThe tool predicts regions that can potentially function as binding sites. The methods is based on recognition of geometrical and physico-chemical environments that are similar to known binding sites.http://bioinfo3d.cs.tau.ac.il/SiteEngine/siteenginebiotools:siteengineWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMachttp://edamontology.org/operation_2575Protein binding site predictionhttp://www.mybiosoftware.com/siteengine-pairwise-3d-alignment-binding-sites.htmlSoftware cataloguehttp://bioinfo3d.cs.tau.ac.il/SiteEngine/SiteEngine.htmlGeneralhttp://bioinfo3d.cs.tau.ac.il/SiteEngine/help.htmlUser manual10.1016/j.jmb.2004.04.01215147845PMC7126412shulmana@tau.ac.ilhttp://bioinfo3d.cs.tau.ac.il/wk/index.php/Main_PagePersonPrimary contactDeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.2.5Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacPythonC++GPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTML

https://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer file1.2.5https://github.com/BolognaBiocomp/deepsigCommand-line options10.1093/bioinformatics/btx81829280997PMC5946842Primary1.0ELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttp://biocomp.unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactNetPicoRNANeural network predictions of cleavage sites of picornaviral proteases.http://cbs.dtu.dk/services/NetPicoRNA/netpicornabiotools:netpicorna1.0Web applicationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxOtherLegacyFree of charge (with restrictions)http://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2955Sequence reporthttp://edamontology.org/format_2333Binary format

produces neural network predictions of cleavage sites of picornaviral proteaseshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/NetPicoRNA/instructions.phpGeneral10.1002/pro.55600511078931139PMC2143287PrimaryCBSInstituteProviderNikolaj Sorgenfrei Blomnikob@cbs.dtu.dkhttps://orcid.org/0000-0001-7787-7853PersonTREND Protein Evolution FunctionTREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.http://trend.evobionet.com/trend_protein_evolution_functionbiotools:trend_protein_evolution_functionWeb servicehttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/operation_0246Protein domain recognitionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_1900NCBI locus taghttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2385RefSeq accession (protein)

http://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_3464JSON

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3604SVG

http://edamontology.org/data_1245Sequence cluster (protein)http://edamontology.org/format_3464JSON

http://trend.evobionet.com/helpUser manual10.1093/nar/gkaa24332282909PMC7319448Primary10.1093/nar/gkac03435100406PMC8860576OtherCan be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937Vadim Gumerovgumerov.1@osu.eduhttps://orcid.org/0000-0003-1670-7679CofactoryIdentification of Rossmann folds and prediction of FAD, NAD and NADP specificity.http://cbs.dtu.dk/services/Cofactory/cofactorybiotools:cofactory2.1Web applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual format

identifies Rossmann fold sequence domains and predicts their specificity for the cofactors FAD, NAD or NADPhttp://www.cbs.dtu.dk/services/doc/cofactory-1.0.readmeRepositoryhttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/doc/cofactory-1.0.readmeSource codehttp://www.cbs.dtu.dk/services/doc/cofactory-1.0.readmeBinarieshttp://www.cbs.dtu.dk/services/Cofactory/instructions.phpGeneral10.1002/prot.2453624523134PrimaryCBSInstituteProviderThomas Nordahl Petersentnp@cbs.dtu.dkPersonPrimary contactIBM Bioinformatics and Pattern Discovery GroupExtensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.http://cbcsrv.watson.ibm.com/Tspd.htmlibm_pattern_discoverybiotools:ibm_pattern_discoveryWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/operation_0452Indel detectionhttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3761Service discoveryhttp://edamontology.org/operation_0238Sequence motif discovery10.1093/nar/gkf33812060689PMC11728110.1093/bioinformatics/14.1.55952050210.1093/nar/gkg62112824385PMC16902710.1093/nar/gkf46412202776PMC13740510.1006/mben.2000.01511105605910.1093/nar/gkh36715215340PMC44150510786305REPPERTool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats.http://protevo.eb.tuebingen.mpg.de/repperrepperbiotools:repperWeb applicationhttp://edamontology.org/topic_0157Sequence composition, complexity and repeatshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/operation_0379Repeat sequence detectionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0380Repeat sequence organisation analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3092Protein feature detection10.1093/nar/gki40515980460PMC1160166GraBCasTool for predicting granzyme B and caspase cleavage sites.http://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/humangenetik/software/grabcasbiotools:grabcasWeb applicationhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/operation_2575Protein binding site prediction10.1093/nar/gki43315980455PMC1160194PlantLocWeb server for predicting plant protein subcellular localization by substantiality motif.http://cal.tongji.edu.cn/PlantLoc/plantlocbiotools:plantlocWeb applicationhttp://edamontology.org/topic_0780Plantshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_1775Function analysishttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_1777Protein function prediction10.1093/nar/gkt42823729470PMC3692052HHsenserTool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, it is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies.http://toolkit.tuebingen.mpg.de/hhsenserhhsenserbiotools:hhsenserWeb applicationhttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0259Sequence alignment comparisonhttp://edamontology.org/operation_0448Sequence alignment analysis (conservation)10.1093/nar/gkl19516845029PMC1538784PiRaNhAPredicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.http://www.bioinformatics.sussex.ac.uk/PIRANHApiranhabiotools:piranhaWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/operation_0272Residue interaction predictionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0267Protein secondary structure prediction10.1093/nar/gkq47420507911PMC289609910.1093/bioinformatics/btp25719389733PutracerReliable method to detect automatically structural domains as protein units. This server provides number of domains and domain boundary for a chain with continues-domains.http://bioinf.modares.ac.ir/software/PUTracer/putracerbiotools:putracerWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2406Protein structure analysishttp://www.mybiosoftware.com/putracer-protein-unit-tracer.htmlSoftware cataloguehttp://bioinf.modares.ac.ir/software/PUTracer/General10.1142/s021972001340012x23427994sh.arab@modares.ac.irPersonPrimary contactH-ProtectionWeb application for prediction of residue status to be protected or unprotected from hydrogen-deuterium exchange in a protein chain.http://bioinfo.protres.ru/ogp/h-protectionbiotools:h-protectionWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3542Protein secondary structureLinuxWindowsMachttp://edamontology.org/operation_0272Residue interaction predictionhttp://www.mybiosoftware.com/h-protection-prediction-of-residue-status-to-be-protected-or-unprotected-from-hydrogen-deuterium-exchange.htmlSoftware cataloguehttp://bioinfo.protres.ru/ogp/General10.2174/1874091x0080201007718949078PMC2570557Galzitskaya Oxana Valerianovnaogalzit@vega.protres.ruhttp://bioinfo.protres.ru/?sec=contacts&lang=en&i=OPersonPrimary contactSokolovskiy Igor Vitalievichsokol@phys.protres.ruhttp://bioinfo.protres.ru/?sec=contacts&lang=en&i=OPersonPrimary contactCCCPPThis software computes the void parts of the proteins, i.e. cavities, channels and pockets.http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CCCPPcccppbiotools:cccppCommand-line toolhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxMachttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/cccpp-compute-cavites-channels-pores-and-pockets-in-proteins.htmlSoftware cataloguehttp://petitjeanmichel.free.fr/itoweb.download.cccpp.readmeGeneral10.1093/bioinformatics/btt64424202541Michel Petitjeanmichel.petitjean@univ-paris-diderot.frhttp://petitjeanmichel.free.fr/itoweb.petitjean.htmlPersonPrimary contactiTIS-PseTNCThis web-server was developed to identify Translation initiation site (TIS) by using the physicochemical properties of the pseudo trinucleotide composition.http://lin.uestc.edu.cn/server/iTIS-PseTNCitis-psetncbiotools:itis-psetncWeb applicationhttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMachttp://edamontology.org/operation_0439Translation initiation site predictionhttp://www.mybiosoftware.com/itis-psetnc-identifying-translation-initiation-site-in-human-genes.htmlSoftware cataloguehttp://lin.uestc.edu.cn/server/iTISPseTNC/readmeGeneral10.1016/j.ab.2014.06.02225016190Hao Linhlin@uestc.edu.cnhttp://lin.uestc.edu.cn/PersonPrimary contactProInflamWebserver for the prediction of proinflammatory antigenicity of peptides and proteins.http://metabiosys.iiserb.ac.in/proinflam/index.htmlproinflambiotools:proinflamWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0346Sequence similarity searchhttp://www.mybiosoftware.com/proinflam-prediction-of-proinflamatory-epitopes.htmlSoftware cataloguehttp://metabiosys.iiserb.ac.in/proinflam/guide.phpGeneral10.1186/s12967-016-0928-327301453PMC4908730http://metabiosys.iiserb.ac.in/contact.htmlPersonPrimary contactRaster3DSet of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Output is to pixel image files with 24 bits of color information per pixel.http://skuld.bmsc.washington.edu/raster3d/raster3d.htmlraster3dbiotools:raster3dCommand-line toolhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_0570Structure visualisationhttp://www.mybiosoftware.com/raster3d-3-0-2-generate-high-quality-raster-images-proteins-molecules.htmlSoftware cataloguehttp://skuld.bmsc.washington.edu/raster3d/html/raster3d.htmlGeneral10.1016/s0076-6879(97)77028-918488322merritt@u.washington.eduPersonPrimary contactHIVcleaveWeb-server for predicting HIV protease cleavage sites in proteins.http://www.csbio.sjtu.edu.cn/bioinf/HIV/hivcleavebiotools:hivcleaveWeb applicationhttp://edamontology.org/topic_0781Virologyhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_3092Protein feature detectionhttp://www.mybiosoftware.com/hivcleave-predicting-hiv-protease-cleavage-sites-in-proteins.htmlSoftware cataloguehttp://www.csbio.sjtu.edu.cn/bioinf/HIV/Readme.htmGeneral10.1016/j.ab.2008.01.01218249180Hong-Binhbshen@sjtu.edu.cnhttp://www.csbio.sjtu.edu.cn/PersonPrimary contactMalakiteA program for automatic detection of aligned blocks in multiple protein alignment.http://mouse.belozersky.msu.ru/tools/malakite.htmlmalakitebiotools:malakiteWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://www.mybiosoftware.com/malakite-automatic-detection-of-aligned-blocks-in-a-multiple-protein-alignment.htmlSoftware cataloguehttp://mouse.belozersky.msu.ru/tools/malakite.htmlGeneral10.1142/s021972001000472020556859Russian Foundation for Basic Researchhttp://www.rfbr.ru/rffi/eng/contacts_engPersonPrimary contactSignal-CFAutomated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequenceshttp://www.csbio.sjtu.edu.cn/bioinf/Signal-CF/signal-cfbiotools:signal-cfWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMachttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://www.mybiosoftware.com/signal-cf-predicting-signal-peptides.htmlSoftware cataloguehttp://www.csbio.sjtu.edu.cn/bioinf/Signal-CF/SignalCFReadme.htmGeneral10.1016/j.bbrc.2007.03.16217434148hbshen@sjtu.edu.cnhttp://www.csbio.sjtu.edu.cn/PersonPrimary contactSignal-3LAutomated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences.http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/signal-3lbiotools:signal-3lWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMachttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/signal-3l-a-3-layer-approach-for-predicting-signal-peptides.htmlSoftware cataloguehttp://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/Signal3LReadme.htmGeneral10.1016/j.bbrc.2007.08.14017880924hbshen@sjtu.edu.cnhttp://www.csbio.sjtu.edu.cn/PersonPrimary contactTepiToolThe tool provides prediction of peptides binding to MHC class I and class II molecules.http://tools.iedb.org/tepitool/tepitoolbiotools:tepitoolWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMachttp://edamontology.org/operation_2575Protein binding site predictionhttp://www.mybiosoftware.com/tepitool-computational-prediction-of-t-cell-epitope-candidates.htmlSoftware cataloguehttp://tools.iedb.org/tepitool/help/General10.1002/cpim.1227479659PMC4981331help@iedb.orghttp://tools.iedb.org/tepitool/contact/PersonPrimary contactUniAlignProtein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles, and residue conservation.http://sacan.biomed.drexel.edu/unialignunialignbiotools:unialignWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://www.mybiosoftware.com/unialign-protein-pairwise-structure-alignment-with-evolution-and-sequence-information.htmlSoftware cataloguehttp://sacan.biomed.drexel.edu/unialign/General10.1093/bioinformatics/btv35426059715ahmet.sacan@drexel.eduhttp://sacan.biomed.drexel.edu/ahmetPersonPrimary contactSODOCKAn optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. PSO is a population-based search algorithm.http://140.113.239.45/sodock/sodockbiotools:sodockCommand-line toolhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3524Simulation experimentLinuxhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://www.mybiosoftware.com/sodock-swarm-optimization-for-flexible-protein-ligand-docking.htmlSoftware cataloguehttp://140.113.239.45/sodock/General10.1002/jcc.2054217186483syho@mail.nctu.edu.twhttp://140.113.239.45/PersonPrimary contactSubPhosPredWeb server that could predict phosphosrylation sites in different subcellular compartments (SCs) of homo sapiens, which combines a novel discrete wavelet transform (DWT) strategy with support vector machine (SVM) approach to identify phosphorylation sites for different SCs in human.http://bioinfo.ncu.edu.cn/SubPhosPred.aspxsubphospredbiotools:subphospredWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3092Protein feature detectionhttp://www.mybiosoftware.com/subphospred-prediction-of-phosphosrylation-sites.htmlSoftware cataloguehttp://bioinfo.ncu.edu.cn/SubPhosHelp.aspxGeneral10.1093/bioinformatics/btu59825236462jdqiu@ncu.edu.cnhttp://bioinfo.ncu.edu.cn/PersonPrimary contactTangoA computer algorithm for prediction of aggregating regions in unfolded polypeptide chains. The model used here, is designed to predict cross-beta aggregation in peptides and denatured proteins and consists of a phase-space encompassing the random coil and 4 possible structural states: beta-turn, alpha-helix, beta-sheet aggregation and alpha-helical aggregation.http://tango.crg.es/tangobiotools:tangoCommand-line toolhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0081Structure analysisLinuxWindowshttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0474Protein structure predictionhttp://www.mybiosoftware.com/tango-2-3-1-prediction-b-sheet-aggregation-unfolded-polypeptide-chains.htmlSoftware cataloguehttp://tango.crg.es/Tango_Handbook.pdfGeneral10.1038/nbt101215361882http://tango.crg.es/support.jspPersonPrimary contactNeuropredNeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.http://stagbeetle.animal.uiuc.edu/cgi-bin/neuropred.pyneuropredbiotools:neuropredWeb applicationhttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_0417Protein post-translation modification site predictionhttp://edamontology.org/operation_0422Protein cleavage site prediction10.1093/nar/gkl16116845008PMC153882510.1021/pr034046d14692459Jonathan V. Sweedlerjsweedle@illinois.eduPersonPrimary contactMoDPepIntNew, easy-to-use webserver for the prediction of binding partners for modular protein domains. The server comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively.http://modpepint.informatik.uni-freiburg.de/modpepintbiotools:modpepintWeb servicehttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacShellC++Perlhttp://edamontology.org/operation_3760Service managementhttp://www.mybiosoftware.com/modpepint-3-3-2-prediction-of-modular-domain-peptide-interactions.htmlSoftware cataloguehttp://modpepint.informatik.uni-freiburg.de/Help.jspGeneral10.1093/bioinformatics/btu35024872426PMC4155253Rolf Backofenbackofen@informatik.uni-freiburg.dehttp://www.bioinf.uni-freiburg.de//?enPersonPrimary contacthttp://modpepint.informatik.uni-freiburg.de/EmailNotification.jspPersonPrimary contactiPACNovel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.http://bioconductor.org/packages/release/bioc/html/iPAC.htmlipacbiotools:ipac1.18.0Command-line toolLibraryhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacRGPL-2.0BioConductorhttp://edamontology.org/operation_3202Polymorphism detectionhttp://bioconductor/packages/release/bioc/src/contrib/iPAC_1.18.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/iPAC.htmlUser manual10.1186/1471-2105-14-19023758891PMC3691676PrimaryGregory Ryslikgregory.ryslik@yale.eduPersonPrimary contactcleaverIn-silico cleavage of polypeptide sequences.http://bioconductor.org/packages/release/bioc/html/cleaver.htmlcleaverbiotools:cleaver1.12.0Command-line toolLibraryhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacRGPL-3.0BioConductorhttp://edamontology.org/operation_0422Protein cleavage site predictionhttps://github.com/sgibb/cleaver/Mirrorhttp://bioconductor/packages/release/bioc/src/contrib/cleaver_1.12.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/cleaver.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherSebastian Gibbmail@sebastiangibb.dePersonPrimary contactSadicThis server is able to calculate the atom depth value for every atom of a protein structure, giving a lot of intrinsic information of 3D composition of the macromolecule and its core.http://www.sbl.unisi.it/prococoa/sadicbiotools:sadicWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacPythonChttp://edamontology.org/operation_0250Protein property calculationhttp://www.mybiosoftware.com/sadic-prococoa-1-1b10-simple-atom-depth-index-calculator-protein-core-composition-analyzer.htmlSoftware cataloguehttp://www.sbl.unisi.it/prococoa/General10.1016/j.compbiolchem.2012.12.00723333734neri.niccolai@unisi.ithttp://www.sbl.unisi.it/PersonPrimary contactSOCKETThe tool finds the Knobs-into-Holes mode of packing between alpha-helices which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script if required.http://coiledcoils.chm.bris.ac.uk/socket/socketbiotools:socketCommand-line toolWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacChttp://edamontology.org/operation_0474Protein structure predictionhttp://www.mybiosoftware.com/socket-3-03-identifies-knobs-into-holes-packing-protein-structures.htmlSoftware cataloguehttp://coiledcoils.chm.bris.ac.uk/socket/READMEGeneralhttp://coiledcoils.chm.bris.ac.uk/socket/manual.txtUser manual10.1006/jmbi.2001.454511292353john.walshaw@bbsrc.ac.ukhttp://www.chm.bris.ac.uk/org/woolfson/index.htmlPersonPrimary contactg.bartlett@bristol.ac.ukPersonPrimary contactMinmotif MinerAnalyzes protein queries for the presence of short contiguous peptide motifs that have a known function in at least one other protein (Minimotifs), its functions include posttranslational modification of the minimotifs (PTM), binding to a target protein or molecule, and protein trafficking. MnM 3.0 uses a rich semantic model and trained algorithm to reduce false positive predictions.http://minimotifminer.orgminmotif_minerbiotools:minmotif_minerWeb applicationhttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0154Small moleculesLinuxWindowsMachttp://edamontology.org/operation_0417Post-translation modification site predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/operation_0253Sequence feature detection10.1038/nmeth8561648933310.1093/nar/gkn86518978024PMC268657910.1093/nar/gkr118922146221PMC3245078SitExDatabase that contains information on functional site amino acid positions in the exon structure of encoding gene. It contains BLAST and 3DExonScan programs. BLAST is used for searching sequence similarity between the query protein and polypeptides encoded by single exons stored in it. The 3DExonScan program is used for searching for structural similarity of the given protein with these polypeptides using superimpositions.http://www-bionet.sscc.ru/sitex/sitexbiotools:sitexDatabase portalhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0154Small moleculesLinuxWindowsMacSQLhttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_3092Protein feature detectionhttp://www-bionet.sscc.ru/sitex/index.phpGeneral10.1093/nar/gkr118722139920PMC3245165Irina Medvedevabrukaro@bionet.nsc.ruPersonPrimary contactVPLGThis uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, e.g. usually alpha helices and beta sheets) or ligand molecules while the edges model contacts and spatial relations between them.http://www.bioinformatik.uni-frankfurt.de/tools/vplg/index.htmlvplgbiotools:vplgCommand-line toolhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavahttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/vplg-20130325-visualization-of-protein-ligand-graphs-software-package.htmlSoftware cataloguehttp://www.bioinformatik.uni-frankfurt.de/tools/vplg/index.html#DocumentationGeneral10.1093/bioinformatics/btv57426446136ina.koch@bioinformatik.uni-frankfurt.dehttp://www.bioinformatik.uni-frankfurt.de/PersonPrimary contactAquariaSimplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...).http://aquaria.wsaquariabiotools:aquaria1Web APIWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMacJavaScriptJavaGPL-2.0Odonoghuelab toolsRostlab toolsMatureFree of chargehttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_1063Sequence identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1869Organism identifierhttp://edamontology.org/format_2330Textual formatYou can find sequences based on a keyword search. For the identified sequence, Aquaria retrieves sequence-to-structure alignments from the PSSH2 database and visualises those on the web page. At the same time, a selected alignment is visualised in the 3D viewer (by default the one with most identical residues between sequence and structure). accession number, ID or part of the name or alias from UniProt Organism names used in UniProt; Homo sapiens used by defaulthttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_1096Sequence accession (protein)http://edamontology.org/format_1963UniProtKB format

http://edamontology.org/data_0893Sequence-structure alignmenthttp://edamontology.org/format_3464JSON

web service to get matching structures with alignment data for a given protein sequence Uniprot accession of query protein glued into the query URL: aquaria.ws/<UniprotAcc>.json json representation of one or more sequence-to-structure alignments annotated with alignment statisticshttps://github.com/ODonoghueLab/AquariaRepositoryhttp://aquaria.ws/help/Aquaria3D_QR_v1.pdfSource codehttp://aquaria.ws/help/Aquaria3D_QR_v1.pdfBinarieshttps://www.youtube.com/watch?v=FAQ3yVGYSzY&feature=youtu.beGeneral10.1038/nmeth.325825633501PrimaryChristian StoltePersonDeveloperKenneth S SabirPersonDeveloperSeán I O'DonoghuePersonDeveloperAndrea SchafferhansPersonDeveloperNelson PerdigãoContributorBurkhard RostContributorVivian HoContributorManfred RoosContributorBenjamin WellmannContributorJulian HeinrichContributorMaria KalemanovContributorFabian A BuskeContributorDepartment for Bioinformatics and Computational Biology, Technische Universität MünchenInstituteProviderDivision of Genomics and Epigenetics, Garvan Institute of Medical Research, SydneyInstituteProviderDigital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), SydneyInstituteProviderSchool of Molecular Bioscience, The University of SydneyInstituteProviderAmazon AWSConsortiumCSIRO's OCE Science Leader program and its Computational and Simulation Sciences platformFunding agencyContributorAlexander von Humboldt FoundationFunding agencyContributorRostLabInstituteProviderSeán I. O'Donoghuesean@odonoghuelab.orgSupportAndrea Schafferhansandrea.schafferhans@rostlab.orgSupportSeán O'Donoghuesean@odonoghuelab.orgPersonPrimary contactAndrea Schafferhansandrea.schafferhans@rostlab.orgPersonPrimary contactSTING MilleniumSTING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/sting_milleniumbiotools:sting_milleniumWeb applicationhttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0081Structure analysisLinuxWindowsMacJavaScriptC++Perlhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2414Protein function analysishttp://edamontology.org/operation_2416Protein secondary structure analysishttp://edamontology.org/operation_2406Protein structure analysishttp://sms.cbi.cnptia.embrapa.br/SMS/STINGm/User manual10.1093/nar/gki39715980473PMC116015810.1093/bioinformatics/bth2031507300110.1093/bioinformatics/bth1901504423210.1093/nar/gki11115608194PMC54006510.1093/bioinformatics/bth1851504423610.1093/protein/13.3.1671077565810.1186/1471-2105-5-10715301693PMC51460110.1093/nar/gkh48015215458PMC44161810.1093/nar/gkg57812824333PMC168984Neshich G.neshich@cnptia.embrapa.brPersonPrimary contactFragHMMentResidue-residue contact prediction.http://predictioncenter.org/Services/FragHMMent/descr.htmlfraghmmentbiotools:fraghmment1Web applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavahttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://predictioncenter.org/Services/FragHMMent/descr.htmlGeneral10.1093/bioinformatics/btp14919289446PMC2677742Primarybils.seInstituteProvidertorgeir.hvidsten@umu.sePersonPrimary contactSCPSRMCyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. This tool contains the scripts used to search for CDK clusters.http://www.moseslab.csb.utoronto.ca/alan/protein_motifs.htmlscpsrmbiotools:scpsrmWeb applicationhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0166Protein structural motifs and surfacesLinuxWindowsMachttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_0245Protein structural motif recognitionhttp://www.moseslab.csb.utoronto.ca/alan/protein_motifs.htmlGeneral10.1186/gb-2007-8-2-r2317316440PMC1852407Alan M Mosesam8@sanger.ac.ukPersonPrimary contactTreeDetTree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.http://treedetv2.bioinfo.cnio.es/treedet/index.htmltreedetbiotools:treedetWeb applicationhttp://edamontology.org/topic_1775Function analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0082Structure predictionPHPPerlFortranChttp://edamontology.org/operation_0272Residue interaction predictionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/operation_0292Sequence alignment10.1093/nar/gkl20316844971PMC153878910.1016/s0022-2836(02)01451-11258976910.1038/nsb0295-171774992110.1093/bioinformatics/bth03214764569TreeDet Supportpazos@cnb.csic.esPersonPrimary contactSeqVISTATool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.http://zlab.bu.edu/SeqVISTA/seqvistabiotools:seqvistaWeb applicationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavahttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0256Sequence feature comparisonhttps://zlab.bu.edu/SeqVISTA/tutorials/index.htmGeneral10.1186/1471-2105-4-112513700PMC14003710.1093/nar/gkh48315215387PMC441621Zhenjun Huzjhu@bu.eduPersonPrimary contactMartin Frithmfrith@bu.eduPersonPrimary contactTianhua Niuniu@bioinfo.stat.harvard.eduPersonPrimary contactZhiping Wengzhiping@bu.eduPersonPrimary contactSplicePortSplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.http://spliceport.cbcb.umd.edu/spliceportbiotools:spliceportWeb applicationhttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_2815Human biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsLinuxWindowsMachttp://edamontology.org/operation_0264Splice transcript predictionhttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/operation_3092Protein feature detectionhttp://spliceport.cbcb.umd.edu/browser_help.htmlGeneral10.1093/nar/gkm40717576680PMC1933122spliceport Supportrezarta@cs.umd.eduPersonPrimary contactINTREPIDThe 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.https://github.com/berkeleyphylogenomics/intrepidintrepidbiotools:intrepidWeb applicationhttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_1775Function analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacPerlPythonhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0272Residue interaction predictionhttp://edamontology.org/operation_0321Protein model validationhttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/operation_0474Protein structure predictionhttps://github.com/benedictpaten/pecan/blob/master/README.mdGeneral10.1093/nar/gkp33919443452PMC2703888Kimmen Sjölanderkimmen@berkeley.eduPersonPrimary contactCHOPCHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.https://rostlab.org/owiki/index.php/CHOPPERchopbiotools:chopWeb applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0157Sequence composition, complexity and repeatsLinuxhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0366Protein sequence cleavagehttp://edamontology.org/operation_0303Protein fold recognitionhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2451Sequence comparisonhttps://rostlab.org/owiki/index.php/Debian_repository#Installing_a_package_step_by_stepGeneral10.1093/nar/gkh48115215452PMC441619Burkhard Rostrost@columbia.eduPersonPrimary contact