NetSurfP-3.0Accurate and fast prediction of protein structural features by protein language models and deep learning.https://services.healthtech.dtu.dk/service.php?NetSurfP-3.0netsurfp-3.0biotools:netsurfp-3.0Web applicationhttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_0082Structure predictionMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_2488Protein secondary structure comparisonhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_0249Protein geometry calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttps://dtu.biolib.com/nsp3Other10.1093/NAR/GKAC43935648435PMC9252760Paolo Marcatilipaolo.marcatili@gmail.comhttps://orcid.org/0000-0003-2615-5695PersonJeppe Hallgrenhttps://orcid.org/0000-0001-5377-2643Henrik Nielsenhttps://orcid.org/0000-0002-9412-9643Ole Wintherhttps://orcid.org/0000-0002-1966-3205Morten Nielsenhttps://orcid.org/0000-0001-7885-4311Bent Petersenhttps://orcid.org/0000-0002-2472-8317Magnus Haraldson Høiehttps://orcid.org/0000-0003-2567-758XErik Nicolas KiehlNetSolPPrediction of solubility and usability of proteins expressed in E. colihttps://services.healthtech.dtu.dk/service.php?NetSolPnetsolpbiotools:netsolpWeb applicationhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_3068Literature and languageMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_0409Protein solubility predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA10.1093/BIOINFORMATICS/BTAB80134849581Alexander Rosenberg Johansenhttps://orcid.org/0000-0002-4993-7916Henrik Nielsenhttps://orcid.org/0000-0002-9412-9643Jose J Almagro Armenteroshttps://orcid.org/0000-0003-0111-1362SignalPPrediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.http://cbs.dtu.dk/services/SignalP/signalpbiotools:signalp4.1rrid:SCR_015644rridCommand-line toolWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxMacOtherCBSMatureFree of charge (with restrictions)http://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2305GFFhttp://edamontology.org/data_2955Sequence reportpredicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organismshttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpRepositoryhttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpSource codehttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpBinarieshttp://www.cbs.dtu.dk/services/SignalPGeneral10.1038/nmeth.170121959131PrimaryTN PetersenPersonDeveloperCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643DeveloperHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactTatPPrediction of the presence and location of Twin-arginine signal peptide cleavage sites in bacteria.http://cbs.dtu.dk/services/TatP/tatpbiotools:tatp1.0Web applicationWeb servicehttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2955Sequence reporthttp://edamontology.org/format_2333Binary formatpredicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria. Signal peptide/non-signal peptide prediction based on a combination of two artificial neural networkshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/TatP/instructions.phpGeneral10.1186/1471-2105-6-16715992409PMC1182353PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactNetAcetPrediction of substrates of N-acetyltransferase A (NatA).http://cbs.dtu.dk/services/NetAcet/netacetbiotools:netacet1.0Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual formatpredicts substrates of N-acetyltransferase A (NatA)http://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/NetAcet/General10.1093/bioinformatics/bti13015539450PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary contactNicolaj Sorgenfrei Blomnblom@kt.dtu.dkhttp://orcid.org/0000-0001-7787-7853PersonSecretomePPredictions of non-classical (i.e. not signal peptide triggered) protein secretion.http://cbs.dtu.dk/services/SecretomeP/secretomepbiotools:secretomep2.0Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual formatpredicts of non-classical protein secretionhttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/SecretomeP/instructions.phpGeneral10.1093/protein/gzh03715115854Primary16212653OtherCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary contactNikolaj Sorgenfrei Blomnblom@kt.dtu.dkhttp://orcid.org/0000-0001-7787-7853PersonTargetPPrediction of the subcellular location of eukaryotic proteins.http://cbs.dtu.dk/services/TargetP/targetpbiotools:targetp1.1Command-line toolWeb applicationWeb servicehttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual formatPredicts the subcellular location of eukaryotic proteinshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/TargetP/instructions.phpGeneral10.1006/jmbi.2000.390310891285PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactChloroPPrediction of presence of chloroplast transit peptides and their cleavage sites in plant proteins.http://cbs.dtu.dk/services/ChloroP/chloropbiotools:chlorop1.1Command-line toolWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacOtherMatureFree of charge (with restrictions)http://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual formatpredicts the presence of chloroplast transit peptides (cTP)http://www.cbs.dtu.dk/services/doc/chlorop-1.1.readmeRepositoryhttp://www.cbs.dtu.dk/services/doc/chlorop-1.1.readmeSource codehttp://www.cbs.dtu.dk/services/doc/chlorop-1.1.readmeBinarieshttp://www.cbs.dtu.dk/services/ChloroPCitation instructionshttp://www.cbs.dtu.dk/services/ChloroP/pages/instr.phpGeneral10.1110/ps.8.5.97810338008PMC2144330Primary10.1110/ps.8.5.97810338008PMC2144330OtherCBSInstituteProviderhttp://www.bioinformatics.dtu.dk/english/Service/ContactPersonPrimary contactHenrik Nielsenhnielsen@bioinformatics.dtu.dkhttp://orcid.org/0000-0002-9412-9643DeepLocPrediction of eukaryotic protein subcellular localization using deep learning.http://www.cbs.dtu.dk/services/DeepLoc/deeplocbiotools:deeploc1.0Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacOtherMaturehttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2331HTMLhttp://edamontology.org/data_2884Plothttp://edamontology.org/format_3603PNGhttp://www.cbs.dtu.dk/services/DeepLoc/instructions.phpUser manual10.1093/bioinformatics/btx431Henrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary contactLocTree3Prediction of protein subcellular localization in 18 classes for eukaryota, 6 for bacteria and 3 for archaea.https://rostlab.org/services/loctree3/loctree3biotools:loctree31.0.8Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_2229Cell biologyLinuxPHPJavaPerlJavaScriptGPL-3.0Rostlab toolsPredictProteinMatureFree of chargehttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSVPrediction of protein sucellular localization in 18 classes for eukaryota, 6 classes for bacteria and 3 for archaea using homology searches (PSI-BLAST) and machine learning (SVM) User can provide one or more sequences in FASTA format The prediction output contains: prediction score, from 1 (weak prediction) to 100 (strong prediction); one of 18 localization classes for eukaryota, 6 for bacteria and 3 for archaea; GO identifier; GO term; prediction source (PSI-BLAST or SVM)https://rostlab.org/owiki/index.php/PackagesRepositoryhttps://rostlab.org/owiki/index.php/PackagesSource codehttps://rostlab.org/owiki/index.php/PackagesBinarieshttps://rostlab.org/owiki/index.php/Loctree3General10.1093/nar/gku396Primary10.1093/bioinformatics/bts390OtherMaximilian HechtPersonDeveloperGuy YachdavPersonDeveloperTimothy KarlPersonDeveloperTobias HampPersonDeveloperTatyana GoldbergPersonDeveloperBurkhard RostContributorHenrik NielsenContributorTechnische Universität MünchenInstituteProviderAlexander von Humboldt Foundation through German Federal Ministry for Education and ResearchFunding agencyContributorErnst Ludwig Ehrlich StudienwerkFunding agencyContributorRostLabInstituteProviderlocalization@rostlab.orghttps://rostlab.org/services/loctree3/PersonPrimary contact