DeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.0Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacGPL-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 formathttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLhttps://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer filehttps://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 contactSNPs and GOA server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.s.http://snps-and-go.biocomp.unibo.it/snps-and-go/index.htmlsnps_and_gobiotools:snps_and_go1.0Web applicationhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRD-connectRare DiseaseBologna Biocomputing GroupMatureFree of chargeOpen accessRare DiseasesItalyhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2414Protein function analysishttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2330Textual formatPredictionhttp://snps-and-go.biocomp.unibo.it/snps-and-go/help2.htmGeneral10.1002/humu.21047PrimaryELIXIR-ITA-BOLOGNAInstituteProviderRita Casadiorita.casadio@unibo.itPersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactTPpred 3.0Organelle-targeting peptide detection and cleavage-site prediction.http://tppred3.biocomp.unibo.ittppred_3.0biotools:tppred_3.03Web applicationCommand-line toolhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0140Protein targeting and localisationhttp://edamontology.org/topic_0154Small moleculesLinuxWindowsMacGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLPredictio Protein sequence in FASTA formathttps://github.com/BolognaBiocomp/tppred3Source codehttps://hub.docker.com/r/bolognabiocomp/tppred3Container filehttps://tppred3.biocomp.unibo.it/tppred3/default/helpGeneralhttps://github.com/BolognaBiocomp/tppred3Command-line optionstppred_2.0isNewVersionOftppred_1.0isNewVersionOf10.1093/bioinformatics/btv36726079349Primary10.1093/bioinformatics/btu41124974200Other10.1093/bioinformatics/btt08923428638Other10.1007/978-1-0716-1262-0_2834118055ReviewBenchmarking studyELIXIR-ITA-BOLOGNAInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttp://biocomp.unibo.it/savojard/https://orcid.org/0000-0002-7359-0633PersonPrimary contactDeveloperBUSCAPrediction of protein subcellular localization from sequencehttp://busca.biocomp.unibo.itbuscabiotools:busca1.0Web applicationhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_0269Transmembrane protein predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://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 formathttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3475TSVPrediction of subcellular localization as GO-term and protein features along sequencehttp://busca.biocomp.unibo.itOtherhttp://busca.biocomp.unibo.it/helpHelpdeskhttp://busca.biocomp.unibo.it/helpUser manual10.1093/nar/gky32029718411PMC6031068PrimaryELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperCastrense Savojardocastrense.savojardo2@unibo.ithttp://biocomp.unibo.it/savojardhttps://orcid.org/0000-0002-7359-0633PersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttp://biocomp.unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactGPCRsclassTool for predicting amine-binding receptors based on a protein sequence provided by the user.http://webs.iiitd.edu.in/raghava/gpcrsclass/gpcrsclassbiotools:gpcrsclassWeb 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 predictionLinuxWindowsMacgpcrhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0269Transmembrane protein predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://webs.iiitd.edu.in/raghava/gpcrsclass/help.htmlGeneral15980444G.P.S. Raghavaraghava@iiitd.ac.inPersonPrimary contactProf Raghava is know to develop open source in bioinformaticsPhobius (EBI)Predict transmembrane topology and signal peptides from the amino acid sequence of a protein.https://www.ebi.ac.uk/jdispatcher/pfa/phobiusphobiusbiotools:phobius1Web applicationWeb servicehttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacEBI ToolsJob Dispatcher Toolshttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0269Transmembrane protein predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1277Protein featureshttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttps://phobius.sbc.su.se/Downloads pagehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttps://www.ebi.ac.uk/jdispatcher/helpGeneralhttps://phobius.sbc.su.se/General10.1016/j.jmb.2004.03.016Primary10.1093/nar/gkac240OtherErik SonnhammerPersonDeveloperStockholm Bioinformatics CenterInstituteProviderEMBL-EBIInstituteProviderJob Dispatcherhttps://www.ebi.ac.uk/jdispatcherProjectPrimary contactBaPreSPredicting bacteriocins using an optimal set of features.https://github.com/suraiya14/BaPreSbapresbiotools:bapresWorkflowhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3510Protein sites, features and motifsRPythonCC-BY-4.0Free of chargeOpen accesshttp://edamontology.org/operation_3482Antimicrobial resistance predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0253Sequence feature detectionhttps://shiny.tricities.wsu.edu/bacteriocin-prediction/Other10.1186/S12859-023-05330-Z37592230PMC10433575Suraiya Akhtersuraiya.akhter@wsu.eduhttps://orcid.org/0000-0001-6577-2034PersonJohn H. Millerjmiller16@wsu.eduPersonDbyDeepExploration of MS detectable peptides via deep learning.https://github.com/BISCodeRepo/DbyDeepdbydeepbiotools:dbydeepCommand-line toolhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3922Proteogenomicshttp://edamontology.org/topic_3510Protein sites, features and motifsPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3643Tag-based peptide identificationhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/operation_0366Protein sequence cleavage10.1021/ACS.ANALCHEM.3C0046037459568PMC10401496Seungjin Nasna@hanyang.ac.krhttps://orcid.org/0000-0002-5159-2048PersonEunok Paekeunokpaek@hanyang.ac.krhttps://orcid.org/0000-0003-3655-9749PersonProtVarProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. Functional and structural annotations, predictions and co-located variants can be explored via an interactive UI or accessed programatically via an API.https://www.ebi.ac.uk/ProtVar/protvarbiotools:protvarWeb applicationWeb APIBioinformatics portalhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_2533DNA mutationhttp://edamontology.org/topic_3510Protein sites, features and motifsMacLinuxWindowsJavaRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_2520DNA mappinghttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_3016VCFhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_2187UniProt-like (text)ProtVar maps missense variants from genomic coordinates to UniProt protein positions in all isoforms.http://edamontology.org/operation_3661SNP annotationhttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_3016VCFhttp://edamontology.org/data_3779Annotated texthttp://edamontology.org/format_2187UniProt-like (text)ProtVar annotates missense variant positions with functional and structural information for the amino acid affected, the protein region and the overall protein role from curated and high throughput sources.https://twitter.com/EBIProtVarSocial mediahttps://docs.google.com/forms/d/e/1FAIpQLSd7P85zRHVspesU3kgF3qWpzSDSYFsyeGFmnkuyzB00HNDmDw/viewform?usp=sf_linkMailing listhttps://www.ebi.ac.uk/ProtVar/helpUser manualThis is a link to the help section in ProtVar with annotated screen shots to help you navigate the tool and understand the data.open_targets_platformusedByuniprotusesuniprotusedByensemblusespdbeusesdbsnpusesclinvarusescrossmapusesalphafold_2useseveusescadd_phredusesJames Stephensonjstephenson@ebi.ac.ukhttps://www.ebi.ac.uk/people/person/james-stephenson/https://orcid.org/0000-0002-6427-5703PersonPrimary contactMaintainerDocumentorEMBL-EBIhttps://www.ebi.ac.uk/InstituteProviderPrabhat Totoohttps://www.ebi.ac.uk/people/person/prabhat-totoo/https://orcid.org/0000-0001-5923-4467PersonDeveloperMaintainerOpen Targetshttps://www.opentargets.org/ConsortiumProFeatMapPython based program creating highly customizable 2D maps showing elements of interests (domains, repeats, PTM sites,...) called feature as defined in Uniprot.https://profeatmap.pythonanywhere.com/profeatmapbiotools:profeatmapWeb applicationhttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3293PhylogeneticsMacLinuxWindowsPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3937Feature extractionhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_0417PTM site predictionhttps://github.com/profeatmap/ProFeatMapRepository10.1093/BIOADV/VBAD02236936371PMC10023195Goran Bichgoran.bich@igbmc.frPersonYves Nominéyves.nomine@igbmc.frhttps://orcid.org/0000-0002-2912-116XPerson