List of protein subcellular localization prediction tools

Meta subcellular localization predictor of Gram-negative protein. MetaLocGramN is a gateway to a number of primary prediction methods (various types: signal ... Listofproteinsubcellularlocalizationpredictiontools FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Thislistofproteinsubcellularlocalisationpredictiontoolsincludessoftware,databases,andwebservicesthatareusedforproteinsubcellularlocalizationprediction. Sometoolsareincludedthatarecommonlyusedtoinferlocationthroughpredictedstructuralproperties,suchassignalpeptideortransmembranehelices,andthesetoolsoutputpredictionsofthesefeaturesratherthanspecificlocations.Thesesoftwarerelatedtoproteinstructurepredictionmayalsoappearinlistsofproteinstructurepredictionsoftware. Tools[edit] Descriptionssourcedfromtheentryinthehttps://bio.tools/registry(usedunderCC-BYlicense)areindicatedbylink Name Description References URL Year AAIndexLoc Machine-learning-basedalgorithmthatusesaminoacidindextopredictproteinsubcellularlocalizationbasedonitssequence.(bio.toolsentry) [1] http://aaindexloc.bii.a-star.edu.sg/ 2008 APSLAP PredictionofapoptosisproteinsubcellularLocalization [2] 2013 AtSubP AhighlyaccuratesubcellularlocalizationpredictiontoolforannotatingtheArabidopsisthalianaproteome.(bio.toolsentry) [3] http://bioinfo3.noble.org/AtSubP/ 2010 BaCelLo BaCelLoisapredictorforthesubcellularlocalizationofproteinsineukaryotes.(bio.toolsentry) [4] http://gpcr.biocomp.unibo.it/bacello/index.htm 2006 BAR+ BAR+isaserverforthestructuralandfunctionalannotationofproteinsequences(bio.toolsentry) [5] http://bar.biocomp.unibo.it/bar2.0/ 2011 BAR BAR3.0isaserverfortheannotationofproteinsequencesrelyingonacomparativelarge-scaleanalysisontheentireUniProt.WithBAR3.0andasequenceyoucanannotatewhenpossible:function(GeneOntology),structure(ProteinDataBank),proteindomains(Pfam).Alsoifyoursequencefallsintoaclusterwithastructural/somestructuraltemplate/sweprovideanalignmenttowardsthetemplate/templatesbasedontheCluster-HMM(HMMprofile)thatallowsyoutodirectlycomputeyour3Dmodel.ClusterHMMsareavailablefordownloading.(bio.toolsentry) [6][5] https://bar.biocomp.unibo.it/bar3/ 2017 BASys BASys(BacterialAnnotationSystem)isatoolforautomatedannotationofbacterialgenomic(chromosomalandplasmid)sequencesincludinggene/proteinnames,GOfunctions,COGfunctions,possibleparaloguesandorthologues,molecularweights,isoelectricpoints,operonstructures,subcellularlocalization,signalpeptides,transmembraneregions,secondarystructures,3-Dstructures,reactions,andpathways.(bio.toolsentry) [7] http://basys.ca 2005 BOMP Thebeta-barrelOuterMembraneproteinPredictor(BOMP)takesoneormorefasta-formattedpolypeptidesequencesfromGram-negativebacteriaasinputandpredictswhetherornottheyarebeta-barrelintegraloutermembraneproteins.(bio.toolsentry) [8] http://www.bioinfo.no/tools/bomp 2004 BPROMPT BayesianPRedictionOfMembraneProteinTopology(BPROMPT)usesaBayesianBeliefNetworktocombinetheresultsofothermembraneproteinpredictionmethodsforaproteinsequence.(bio.toolsentry) [9] http://www.ddg-pharmfac.net/bprompt/BPROMPT/BPROMPT.html 2003 Cell-PLoc Apackageofweb-serversforpredictingsubcellularlocalizationofproteinsinvariousorganisms. [10] 2008 CELLO CELLOusesatwo-levelSupportVectorMachinesystemtoassignlocalizationstobothprokaryoticandeukaryoticproteins. [11][12] 2006 ClubSub-P ClubSub-Pisadatabaseofcluster-basedsubcellularlocalization(SCL)predictionsforArchaeaandGramnegativebacteria. [13] 2011 CoBaltDB CoBaltDBisanovelpowerfulplatformthatprovideseasyaccesstotheresultsofmultiplelocalizationtoolsandsupportforpredictingprokaryoticproteinlocalizations. [14] 2010 ComiR ComiRisawebtoolforcombinatorialmicroRNA(miRNA)targetprediction.GivenanmessengerRNA(mRNA)inhuman,mouse,flyorwormgenomes,ComiRpredictswhetheragivenmRNAistargetedbyasetofmiRNAs.(bio.toolsentry) [15] http://www.benoslab.pitt.edu/comir/ 2013 cropPAL Adataportaltoaccessthecompendiumofdataoncropproteinsubcellularlocations.(bio.toolsentry) [16] http://crop-pal.org/ 2016 DAS-TMfilter DAS(DenseAlignmentSurface)isbasedonlow-stringencydot-plotsofthequerysequenceagainstasetoflibrarysequences-non-homologousmembraneproteins-usingapreviouslyderived,specialscoringmatrix.Themethodprovidesahighprecisionhyrdophobicityprofileforthequeryfromwhichthelocationofthepotentialtransmembranesegmentscanbeobtained.ThenoveltyoftheDAS-TMfilteralgorithmisasecondpredictioncycletopredictTMsegmentsinthesequencesoftheTM-library.(bio.toolsentry) [17] http://mendel.imp.ac.at/sat/DAS/DAS.html 2002 DeepLoc Predictionofeukaryoticproteinsubcellularlocalizationusingdeeplearning(bio.toolsentry) [18] http://www.cbs.dtu.dk/services/DeepLoc/ 2017 LightAttention Deeplearningarchitectureforpredictingeukaryoticsubcellularlocalizationandwebserverwhichpredicts10locationsforarbitraryamountsofsequencesthatcanbeuploadedas.fastaorcopy-pasted(bio.toolsentry) [19] https://github.com/HannesStark/protein-localization 2021 DIANA-microTv5.0 WebserverwhichpredictstargetsformiRNAsandprovidesfunctionalinformationonthepredictedmiRNA:targetgeneinteractionfromvariousonlinebiologicalresources.UpdatesenabletheassociationofmiRNAstodiseasesthroughbibliographicanalysisandconnectiontotheUCSCgenomebrowser.Updatesincludesophisticatedworkflows.(bio.toolsentry) [20][21] http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=MicroT_CDS/index 2013 DrugBank DrugBankisauniquebioinformatics/cheminformaticsresourcethatcombinesdetaileddrug(i.e.chemical)datawithcomprehensivedrugtarget(i.e.protein)information.Thedatabasecontains>4100drugentriesincluding>800FDAapprovedsmallmoleculeandbiotechdrugsaswellas>3200experimentaldrugs.Additionally,>14,000proteinordrugtargetsequencesarelinkedtothesedrugentries.(bio.toolsentry) [22] http://redpoll.pharmacy.ualberta.ca/drugbank/index.html 2006 E.ColiIndex ComprehensiveguideofinformationrelatingtoE.coli;homeofEchobase:adatabaseofE.coligenescharacterizedsincethecompletionofthegenome.(bio.toolsentry) [23] http://www.york.ac.uk/res/thomas/ 2009 ePlant Asuiteofopen-sourceworldwideweb-basedtoolsforthevisualizationoflarge-scaledatasetsfromthemodelorganismArabidopsisthaliana.Itcanbeappliedtoanymodelorganism.Currentlyhas3modules:asequenceconservationexplorerthatincludeshomologyrelationshipsandsinglenucleotidepolymorphismdata,aproteinstructuremodelexplorer,amolecularinteractionnetworkexplorer,ageneproductsubcellularlocalizationexplorer,andageneexpressionpatternexplorer.(bio.toolsentry) [24] http://bar.utoronto.ca/eplant/ 2011 ESLpred ESLpredisatoolforpredictingsubcellularlocalizationofproteinsusingsupportvectormachines.Thepredictionsarebasedondipeptideandaminoacidcomposition,andphysico-chemicalproperties.(bio.toolsentry) [25] http://www.imtech.res.in/raghava/eslpred/ 2004 Euk-mPLoc2.0 Predictingthesubcellularlocalizationofeukaryoticproteinswithbothsingleandmultiplesites. [26] 2010 HIT AcomprehensiveandfullycurateddatabaseforHerbIngredients??Targets(HIT).Thoseherbalingredientswithproteintargetinformationwerecarefullycurated.Themoleculartargetinformationinvolvesthoseproteinsbeingdirectly/indirectlyactivated/inhibited,proteinbindersandenzymeswhosesubstratesorproductsarethosecompounds.Thoseup/downregulatedgenesarealsoincludedunderthetreatmentofindividualingredients.Inaddition,theexperimentalcondition,observedbioactivityandvariousreferencesareprovidedaswellforuser??sreference.Thedatabasecanbequeriedviakeywordsearchorsimilaritysearch.CrosslinkshavebeenmadetoTTD,DrugBank,KEGG,PDB,Uniprot,Pfam,NCBI,TCM-IDandotherdatabases.(bio.toolsentry) [27] http://lifecenter.sgst.cn/hit/ 2011 HMMTOP Predictionoftransmembraneshelicesandtopologyofproteins.(bio.toolsentry) [28][29] http://www.enzim.hu/hmmtop/ 2001 HSLpred Allowspredictingthesubcellularlocalizationofhumanproteins.ThisisbasedonvarioustypeofresiduecompositionofproteinsusingSVMtechnique.(bio.toolsentry) [30] http://www.imtech.res.in/raghava/hslpred/ 2005 idTarget idTargetisawebserverforidentifyingbiomoleculartargetsofsmallchemicalmoleculeswithrobustscoringfunctionsandadivide-and-conquerdockingapproach.idTargetscreensagainstproteinstructuresinPDB.(bio.toolsentry) [31] http://idtarget.rcas.sinica.edu.tw 2012 iLoc-Cell Predictorforsubcellularlocationsofhumanproteinswithmultiplesites.(bio.toolsentry) [32] http://www.jci-bioinfo.cn/iLoc-Hum 2012 KnowPredsite Aknowledge-basedapproachtopredictthelocalizationsite(s)ofbothsingle-localizedandmulti-localizedproteinsforalleukaryotes. [33] 2009 lncRNAdb lncRNAdbdatabasecontainsacomprehensivelistoflongnoncodingRNAs(lncRNAs)thathavebeenshowntohave,ortobeassociatedwith,biologicalfunctionsineukaryotes,aswellasmessengerRNAsthathaveregulatoryroles.EachentrycontainsreferencedinformationabouttheRNA,includingsequences,structuralinformation,genomiccontext,expression,subcellularlocalization,conservation,functionalevidenceandotherrelevantinformation.lncRNAdbcanbesearchedbyqueryingpublishedRNAnamesandaliases,sequences,speciesandassociatedprotein-codinggenes,aswellastermscontainedintheannotations,suchasthetissuesinwhichthetranscriptsareexpressedandassociateddiseases.Inaddition,lncRNAdbislinkedtotheUCSCGenomeBrowserforvisualizationandNoncodingRNAExpressionDatabase(NRED)forexpressioninformationfromavarietyofsources.(bio.toolsentry) [34] http://arquivo.pt/wayback/20160516021755/http://www.lncrnadb.org/ 2011 Loc3D LOC3Disadatabaseofpredictedsubcellularlocalizationforeukaryoticproteinsofknownthree-dimensional(3D)structureandincludestoolstopredictthesubcellularlocalizationforsubmittedproteinsequences.(bio.toolsentry) [35][36][37] http://cubic.bioc.columbia.edu/db/LOC3d/ 2005 LOCATE LOCATEisacurateddatabasethathousesdatadescribingthemembraneorganizationandsubcellularlocalizationofmouseproteins.(bio.toolsentry) [38] https://web.archive.org/web/20171231015119/http://locate.imb.uq.edu.au/ 2006 LocDB LocDBisamanuallycurateddatabasewithexperimentalannotationsforthesubcellularlocalizationsofproteinsinHomosapiens(HS,human)andArabidopsisthaliana(AT,thalecress).EachdatabaseentrycontainstheexperimentallyderivedlocalizationinGeneOntology(GO)terminology,theexperimentalannotationoflocalization,localizationpredictionsbystate-of-the-artmethodsand,whereavailable,thetypeofexperimentalinformation.LocDBissearchablebykeyword,proteinnameandsubcellularcompartment,aswellasbyidentifiersfromUniProt,EnsemblandTAIRresources.(bio.toolsentry) [39] http://www.rostlab.org/services/locDB/ 2011 LOCtarget LOCtargetisatoolforpredicting,andadatabaseofpre-computedpredictionsfor,sub-cellularlocalizationofeukaryoticandprokaryoticproteins.Severalmethodsareemployedtomakethepredictions,includingtextanalysisofSWISS-PROTkeywords,nuclearlocalizationsignals,andtheuseofneuralnetworks.(bio.toolsentry) [40] http://www.rostlab.org/services/LOCtarget/ 2004 LOCtree Predictionbasedonmimickingthecellularsortingmechanismusingahierarchicalimplementationofsupportvectormachines.LOCtreeisacomprehensivepredictorincorporatingpredictionsbasedonPROSITE/PFAMsignaturesaswellasSwissProtkeywords. [36] 2005 LocTree2 Frameworktopredictlocalizationinlife'sthreedomains,includingglobularandmembraneproteins(3classesforarchaea;6forbacteriaand18foreukaryota).Theresultingmethod,LocTree2,workswellevenforproteinfragments.Itusesahierarchicalsystemofsupportvectormachinesthatimitatesthecascadingmechanismofcellularsorting.Themethodreacheshighlevelsofsustainedperformance(eukaryota:Q18=65%,bacteria:Q6=84%).LocTree2alsoaccuratelydistinguishesmembraneandnon-membraneproteins.Inourhands,itcomparedfavorablywithtopmethodswhentestedonnewdata(bio.toolsentry) [41] https://rostlab.org/owiki/index.php/Loctree2 2012 LocTree3 Predictionofproteinsubcellularlocalizationin18classesforeukaryota,6forbacteriaand3forarchaea(bio.toolsentry) [41][42] https://rostlab.org/services/loctree3/ 2014 MARSpred PredictionmethodÂfordiscriminationbetweenMitochondrial-AARSsandCytosolic-AARSs.(bio.toolsentry) [43] http://www.imtech.res.in/raghava/marspred/ 2012 MDLoc Dependency-BasedProteinSubcellularLocationPredictor.(bio.toolsentry) [44] http://128.4.31.235/ 2015 MemLoci Predictorforthesubcellularlocalizationofproteinsassociatedorinsertedineukaryotesmembranes.(bio.toolsentry) [45] https://mu2py.biocomp.unibo.it/memloci 2011 MemPype PredictionoftopologyandsubcellularlocalizationofEukaryoticmembraneproteins.(bio.toolsentry) [46] https://mu2py.biocomp.unibo.it/mempype 2011 MetaLocGramN MetasubcellularlocalizationpredictorofGram-negativeprotein.MetaLocGramNisagatewaytoanumberofprimarypredictionmethods(varioustypes:signalpeptide,beta-barrel,transmembranehelicesandsubcellularlocalizationpredictors).Inauthor'sbenchmark,MetaLocGramNperformedbetterincomparisontootherSCLpredictivemethods,sincetheaverageMatthewscorrelationcoefficientreached0.806thatenhancedthepredictivecapabilityby12%(comparedtoPSORTb3).MetaLocGramNcanberunviaSOAP. [47] 2012 MirZ MirZisawebserverthatforevaluationandanalysisofmiRNA.ItintegratestwomiRNAresources:thesmiRNAdbmiRNAexpressionatlasandtheE1MMomiRNAtargetpredictionalgorithm.(bio.toolsentry) [48] http://www.mirz.unibas.ch 2009 MitPred Web-serverspecificallytrainedtopredicttheproteinswhicharedestinedtolocalizedinmitochondriainyeastandanimalsparticularly.(bio.toolsentry) [49] http://www.imtech.res.in/raghava/mitpred/ 2006 MultiLoc AnSVM-basedpredictionengineforawiderangeofsubcellularlocations. [50] 2006 Mycosub Thisweb-serverwasusedtopredictthesubcellularlocalizationsofmycobacterialproteinsbasedonoptimaltripeptidecompositions.(bio.toolsentry) [51] http://lin.uestc.edu.cn/server/Mycosub 2015 NetNES Predictionoftheleucine-richnuclearexportsignals(NES)ineukaryoticproteins(bio.toolsentry) [52] http://cbs.dtu.dk/services/NetNES/ 2004 ngLOC ngLOCisann-gram-basedBayesianclassifierthatpredictssubcellularlocalizationofproteinsbothinprokaryotesandeukaryotes.Theoverallpredictionaccuracyvariesfrom85.3%to91.4%acrossspecies.(bio.toolsentry) [53] http://genome.unmc.edu/ngLOC/index.html 2007 OBCOL Softwarewedesignedtoperformorganelle-basedcolocalisationanalysisfrommulti-fluorophoremicroscopy2D,3Dand4Dcellimaging.(bio.toolsentry) [54] http://obcol.imb.uq.edu.au/ 2009 PA-SUB PA-SUB(ProteomeAnalystSpecializedSubcellularLocalizationServer)canbeusedtopredictthesubcellularlocalizationofproteinsusingestablishedmachinelearningtechniques.(bio.toolsentry) [55][56] http://www.cs.ualberta.ca/~bioinfo/PA/Sub/ 2004 PharmMapper PharmMapperisawebserverthatidentifiespotentialdrugtargetsfromitsPharmTargetDBforagiveninputmolecule.Potentialtargetsareidentifiedfromapredictionofthespatialarrangementoffeaturesessentialforagivenmoleculetointeractwithatarget.(bio.toolsentry) [57] http://59.78.96.61/pharmmapper 2010 PlantLoc PlantLocisawebserverforpredictingplantproteinsubcellularlocalizationbysubstantialitymotif.(bio.toolsentry) [58] http://cal.tongji.edu.cn/PlantLoc/ 2013 PRED-TMBB PRED-TMBBisatoolthattakesaGram-negativebacteriaproteinsequenceasinputandpredictsthetransmembranestrandsandtheprobabilityofitbeinganoutermembranebeta-barrelprotein.Theuserhasachoiceofthreedifferentdecodingmethods.(bio.toolsentry) [59][60] http://bioinformatics.biol.uoa.gr/PRED-TMBB/ 2004 PredictNLS Predictionandanalysisofnuclearlocalizationsignals(bio.toolsentry) [61] https://www.rostlab.org/owiki/index.php/PredictNLS 2000 PredictProteinOpen Predictionofvariousaspectsofproteinstructureandfunction.Ausermaysubmitaquerytotheserverwithoutregistration.(bio.toolsentry) [62][63][64][65] http://ppopen.informatik.tu-muenchen.de/ 2014 PREPSuite ThePREP(PredictiveRNAEditorsforPlants)suitepredictssitesofRNAeditingbasedontheprinciplethateditinginplantorganellesincreasestheconservationofproteinsacrossspecies.Predictorsformitochondrialgenes,chloroplastgenes,andalignmentsinputbytheuserareincluded.(bio.toolsentry) [66][67] http://prep.unl.edu/ 2009 ProLoc-GO ProLoc-GOisanefficientsequence-basedmethodbymininginformativeGeneOntologytermsforpredictingproteinsubcellularlocalization.(bio.toolsentry) [68] http://140.113.239.45/prolocgo/ 2008 ProLoc Evolutionarysupportvectormachine(ESVM)basedclassifierwithautomaticselectionfromalargesetofphysicochemicalcomposition(PCC)featurestodesignanaccuratesystemforpredictingproteinsubnuclearlocalization.(bio.toolsentry) [69] http://140.113.239.45/proloc/ 2007 Protegen Protegenisaweb-baseddatabaseandanalysissystemthatcurates,storesandanalyzesprotectiveantigens.Protegenincludesbasicantigeninformationandexperimentalevidencecuratedfrompeer-reviewedarticles.Italsoincludesdetailedgene/proteininformation(e.g.DNAandproteinsequences,andCOGclassification).Differentantigenfeatures,suchasproteinweightandpI,andsubcellularlocalizationsofbacterialproteinsareprecomputed.(bio.toolsentry) [70] http://www.violinet.org/protegen 2011 ProteomeAnalyst ProteomeAnalystisahigh-throughputtoolforpredictingpropertiesforeachproteininaproteome.Theuserprovidesaproteomeinfastaformat,andthesystememploysPsi-blast,PsipredandModellertopredictproteinfunctionandsubcellularlocalization.ProteomeAnalystusesmachine-learnedclassifierstopredictthingssuchasGOmolecularfunction.User-suppliedtrainingdatacanalsobeusedtocreatecustomclassifiers.(bio.toolsentry) [56] http://www.cs.ualberta.ca/~bioinfo/PA/ 2004 ProTox ProToxisawebserverfortheinsilicopredictionoforaltoxicitiesofsmallmoleculesinrodents.(bio.toolsentry) [71][72] http://tox.charite.de/tox 2018 PSLpred Methodforsubcellularlocalizationproteinsbelongstoprokaryoticgenomes.(bio.toolsentry) [73] http://www.imtech.res.in/raghava/pslpred/ 2005 PSORTb PSORTb(for“bacterial”PSORT)isahigh-precisionlocalizationpredictionmethodforbacterialproteins.PSORTbhasremainedthemostprecisebacterialproteinsubcellularlocalization(SCL)predictorsinceitwasfirstmadeavailablein2003.PSORTbversionimprovedrecall,higherproteome-scalepredictioncoverage,andnewrefinedlocalizationsubcategories.ItisthefirstSCLpredictorspecificallygearedforallprokaryotes,includingarchaeaandbacteriawithatypicalmembrane/cellwalltopologies.(bio.toolsentry) [74] http://www.psort.org/psortb/ 2010 PSORTdb PSORTdb(partofthePSORTfamily)isadatabaseofproteinsubcellularlocalizationsforbacteriaandarchaeathatcontainsbothinformationdeterminedthroughlaboratoryexperimentation(ePSORTdbdataset)andcomputationalpredictions(cPSORTdbdataset).(bio.toolsentry) [75][76] http://db.psort.org 2010 psRobot psRobotisaweb-basedtoolforplantsmallRNAmeta-analysis.psRobotcomputesstem-loopsmallRNAprediction,whichalignsuseruploadedsequencestotheselectedgenome,extractstheirpredictedprecursors,andpredictswhethertheprecursorscanfoldintostem-loopshapedsecondarystructure.psRobotalsocomputessmallRNAtargetprediction,whichpredictthepossibletargetsofuserprovidedsmallRNAsequencesfromtheselectedtranscriptlibrary.(bio.toolsentry) [77] http://omicslab.genetics.ac.cn/psRobot/ 2012 pTARGET pTARGETpredictsthesubcellularlocalizationofeukaryoticproteinsbasedontheoccurrencepatternsoflocation-specificproteinfunctionaldomainsandtheaminoacidcompositionaldifferencesinproteinsfromninedistinctsubcellularlocations.(bio.toolsentry) [78][79] http://bioinformatics.albany.edu/~ptarget 2006 RegPhos RegPhosisadatabaseforexplorationofthephosphorylationnetworkassociatedwithaninputofgenes/proteins.Subcellularlocalizationinformationisalsoincluded.(bio.toolsentry) [80] http://regphos.mbc.nctu.edu.tw/ 2011 RepTar RepTarisadatabaseofmiRNAtargetpredictions,basedontheRepTaralgorithmthatisindependentofevolutionaryconservationconsiderationsandisnotlimitedtoseedpairingsites.(bio.toolsentry) [81] http://reptar.ekmd.huji.ac.il 2011 RNApredator RNApredatorisawebserverforthepredictionofbacterialsRNAtargets.Theusercanchoosefromalargeselectionofgenomes.AccessibilityofthetargettothesRNAisconsidered.(bio.toolsentry) [82] http://rna.tbi.univie.ac.at/RNApredator 2011 S-PSorter Anovelcellstructure-drivenclassifierconstructionapproachforpredictingimage-basedproteinsubcellularlocationbyemployingthepriorbiologicalstructuralinformation.(bio.toolsentry) [83] https://github.com/shaoweinuaa/S-PSorter 2016 SChloro Predictionofproteinsub-chloroplastinclocalization.(bio.toolsentry) [84] http://schloro.biocomp.unibo.it 2017 SCLAP AnAdaptiveBoostingMethodforPredictingSubchloroplastLocalizationofPlantProteins. [85] 2013 SCLPred SCLpredproteinsubcellularlocalizationpredictionbyN-to-1neuralnetworks. [86] 2011 SCLpred-EMS SubcellularlocalizationpredictionofendomembranesystemandsecretorypathwayproteinsbyDeepN-to-1ConvolutionalNeuralNetworks [87] http://distilldeep.ucd.ie/SCLpred2/ 2020 SCLpred-MEM SubcellularlocalizationpredictionofmembraneproteinsbydeepN-to-1convolutionalneuralnetworks [88] http://distilldeep.ucd.ie/SCLpred-MEM/ 2021 SecretomeP Predictionsofnon-classical(i.e.notsignalpeptidetriggered)proteinsecretion(bio.toolsentry) [89][90] http://cbs.dtu.dk/services/SecretomeP/ 2005 SemiBiomarker Newsemi-supervisedprotocolthatcanuseunlabeledcancerproteindatainmodelconstructionbyaniterativeandincrementaltrainingstrategy.Itcanresultinimprovedaccuracyandsensitivityofsubcellularlocationdifferencedetection.(bio.toolsentry) [91] http://www.csbio.sjtu.edu.cn/bioinf/SemiBiomarker/ 2015 SherLoc AnSVM-basedpredictorcombiningMultiLocwithtext-basedfeaturesderivedfromPubMedabstracts. [92] 2007 SUBA3 AsubcellularlocalisationdatabaseforArabidopsisproteins,withonlinesearchinterface.(bio.toolsentry) [93][94] http://suba3.plantenergy.uwa.edu.au/ 2014 SubChlo Computationalsystemforpredictingproteinsubchloroplastlocationsfromitsprimarysequence.Itcanlocatetheproteinwhosesubcellularlocationischloroplastinoneofthefourparts:envelope(whichconsistsofoutermembraneandinnermembrane),thylakoidlumen,stromaandthylakoidmembrane.(bio.toolsentry) [95] http://bioinfo.au.tsinghua.edu.cn/software/subchlo/ 2009 SuperPred TheSuperPredwebservercomparesthestructuralfingerprintofaninputmoleculetoadatabaseofdrugsconnectedtotheirdrugtargetsandaffectedpathways.Asthebiologicaleffectiswellpredictable,ifthestructuralsimilarityissufficient,theweb-serverallowsprognosesaboutthemedicalindicationareaofnovelcompoundsandtofindnewleadsforknowntargets.Suchinformationcanbeusefulindrugclassificationandtargetprediction.(bio.toolsentry) [96] http://bioinformatics.charite.de/superpred 2008 SuperTarget Webresourceforanalyzingdrug-targetinteractions.Integratesdrug-relatedinfoassociatedwithmedicalindications,adversedrugeffects,drugmetabolism,pathwaysandGeneOntology(GO)termsfortargetproteins.(bio.toolsentry) [97] http://bioinformatics.charite.de/supertarget/ 2012 SwissTargetPrediction SwissTargetPredictionisawebserverfortargetpredictionofbioactivesmallmolecules.Thiswebsiteallowsyoutopredictthetargetsofasmallmolecule.Usingacombinationof2Dand3Dsimilaritymeasures,itcomparesthequerymoleculetoalibraryof280000compoundsactiveonmorethan2000targetsof5differentorganisms.(bio.toolsentry) [98][99] http://www.swisstargetprediction.ch 2014 T3DB TheToxinandToxin-TargetDatabase(T3DB)isauniquebioinformaticsresourcethatcompilescomprehensiveinformationaboutcommonorubiquitoustoxinsandtheirtoxin-targets.EachT3DBrecord(ToxCard)containsover80datafieldsprovidingdetailedinformationonchemicalpropertiesanddescriptors,toxicityvalues,proteinandgenesequences(forbothtargetsandtoxins),molecularandcellularinteractiondata,toxicologicaldata,mechanisticinformationandreferences.Thisinformationhasbeenmanuallyextractedandmanuallyverifiedfromnumeroussources,includingotherelectronicdatabases,governmentdocuments,textbooksandscientificjournals.AkeyfocusoftheT3DBisonproviding ??depth??over ??breadth??withdetaileddescriptions,mechanismsofaction,andinformationontoxinsandtoxin-targets.PotentialapplicationsoftheT3DBincludeclinicalmetabolomics,toxintargetprediction,toxicitypredictionandtoxicologyeducation.(bio.toolsentry) [100] http://www.t3db.org 2010 TALE-NT Transcriptionactivator-like(TAL)Effector-NucleotideTargeter2.0(TALE-NT)isasuiteofweb-basedtoolsthatallowsforcustomdesignofTALeffectorrepeatarraysfordesiredtargetsandpredictionofTALeffectorbindingsites.(bio.toolsentry) [101] https://boglab.plp.iastate.edu/ 2012 TarFisDock TargetFishingDock(TarFisDock)isawebserverthatdockssmallmoleculeswithproteinstructuresinthePotentialDrugTargetDatabase(PDTD)inanefforttodiscovernewdrugtargets.(bio.toolsentry) [102] http://www.dddc.ac.cn/tarfisdock/ 2006 TargetRNA TargetRNAisawebbasedtoolforidentifyingmRNAtargetsofsmallnon-codingRNAsinbacterialspecies.(bio.toolsentry) [103] http://cs.wellesley.edu/~btjaden/TargetRNA2/ 2008 TargetP PredictionofN-terminalsortingsignals. [104] 2000 TDRTargets TropicalDiseaseResearch(TDR)Database:Designedanddevelopedtofacilitatetherapididentificationandprioritizationofmoleculartargetsfordrugdevelopment,focusingonpathogensresponsibleforneglectedhumandiseases.Thedatabaseintegratespathogenspecificgenomicinformationwithfunctionaldataforgenescollectedfromvarioussources,includingliteraturecuration.Informationcanbebrowsedandqueried.(bio.toolsentry) [105] http://tdrtargets.org/ 2012 TetraMito Sequence-basedpredictorforidentifyingsubmitochondrialocationofproteins.(bio.toolsentry) [106] http://lin.uestc.edu.cn/server/TetraMito 2013 TMBETA-NET Toolthatpredictstransmembranebetastrandsinanoutermembraneproteinfromitsaminoacidsequence.(bio.toolsentry) [107][108] http://psfs.cbrc.jp/tmbeta-net/ 2005 TMHMM Predictionoftransmembranehelicestoidentifytransmembraneproteins. [109] 2001 TMPred TheTMpredprogrammakesapredictionofmembrane-spanningregionsandtheirorientation.ThealgorithmisbasedonthestatisticalanalysisofTMbase,adatabaseofnaturallyoccurringtransmembraneproteins(bio.toolsentry) [110] http://embnet.vital-it.ch/software/TMPRED_form.html 1993 TPpred1.0 Organelletargetingpeptideprediction(bio.toolsentry) [111] http://tppred.biocomp.unibo.it/tppred/default/index 2013 TPpred2.0 Mitochondrialtargetingpeptideprediction(bio.toolsentry) [112][111] https://tppred3.biocomp.unibo.it 2015 TPpred3.0 Organelle-targetingpeptidedetectionandcleavage-siteprediction(bio.toolsentry) [112] http://tppred3.biocomp.unibo.it/tppred3 2015 TTD TherapeuticTargetDatabase(TTD)hasbeendevelopedtoprovideinformationabouttherapeutictargetsandcorrespondingdrugs.TTDincludesinformationaboutsuccessful,clinicaltrialandresearchtargets,approved,clinicaltrialandexperimentaldrugslinkedtotheirprimarytargets,newwaystoaccessdatabydrugmodeofaction,recursivesearchofrelatedtargetsordrugs,similaritytargetanddrugsearching,customizedandwholedatadownload,andstandardizedtargetID.(bio.toolsentry) [113] http://bidd.nus.edu.sg/group/cjttd/ 2010 UM-PPS TheUniversityofMinnesotaPathwayPredictionSystem(UM-PPS)isawebtoolthatrecognizesfunctionalgroupsinorganiccompoundsthatarepotentialtargetsofmicrobialcatabolicreactionsandpredictstransformationsofthesegroupsbasedonbiotransformationrules.Multi-levelpredictionsaremade.(bio.toolsentry) [114] http://eawag-bbd.ethz.ch/predict/aboutPPS.html 2008 WoLFPSORT WoLFPSORTisanextensionofthePSORTIIprogramforproteinsubcellularlocationprediction.(bio.toolsentry) [115] https://wolfpsort.hgc.jp/ 2007 YLoc 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