Subcellular Localization Prediction Tools

A list of published protein subcellular localization prediction tools. Tool Name, Locations or Protein Features Predicted, Organism Categories ... SubcellularLocalizationPredictionTools MeinkenJ,MinXJ.(2012)Computationalpredictionofproteinsubcellularlocationsineukaryotes:anexperiencereport.ComputationalMolecularBiology.2(1):1-7(doi:10.5376/cmb.2012.02.0001). Alistofpublishedproteinsubcellularlocalizationpredictiontools ToolName LocationsorProteinFeaturesPredicted OrganismCategories PublicationReference TargetP extracellular,mitochondrial,chloroplast non-plant,plant Emanuelsson,O.,Nielsen,H.,Brunak,S.,&vonHeijne,G. (2000) PredictingsubcellularlocalizationofproteinsbasedontheirN-terminalaminoacidsequence. Journalofmolecularbiology, 300(4),1005-1016. TMHMM transmembranehelices any Krogh,A.,Larsson,B.,vonHeijne,G.,&Sonnhammer,E.L. (2001) PredictingtransmembraneproteintopologywithahiddenMarkovmodel:applicationtocompletegenomes. Journalofmolecularbiology, 305(3),567-580. scanProsite(PS-Scan) ERretentionsignal any deCastroE,SigristCJ,GattikerA,BulliardV,Langendijk-GenevauxPS,GasteigerE,BairochA,HuloN. (2006) ScanProsite:detectionofPROSITEsignaturematchesandProRule-associatedfunctionalandstructuralresiduesinproteins. NucleicAcidsRes., 34(WebServerissue),W362-365. SecretomeP2.0 non-classicali.e.notsignalpeptidetriggeredproteinsecretion gram-positivebacteria,gram-negativebacteria,mammal BendtsenJ.D.,Jensen,L.J.,Blom,N.,etal. (2004) Featurebasedpredictionofnon-classicalandleaderlessproteinsecretion. ProteinEng.Des.Sel., 17,349-356. Phobius signalpeptideandtransmembranetopology any Käll,L.,Krogh,A.,&Sonnhammer,E.L.L. (2007) Advantagesofcombinedtransmembranetopologyandsignalpeptideprediction--thePhobiuswebserver.. NucleicAcidsRes., 35(WebServerissue),W429-432. WoLFPSORT >5locations fungi,plant,animal Horton,P.,Park,K.-J.,Obayashi,T.,Fujita,N.,Harada,H.,Adams-Collier,C.J.,&Nakai,K. (2007) WoLFPSORT:proteinlocalizationpredictor. NucleicAcidsRes., 35(WebServerissue),W585-587. PRED-LIPO lipoproteinsignalpeptides gram-positivebacteria Bagos,PantelisG,Tsirigos,K.D.,Liakopoulos,T.D.,&Hamodrakas,S.J. (2008) PredictionoflipoproteinsignalpeptidesinGram-positivebacteriawithaHiddenMarkovModel. Journalofproteomeresearch, 7(12),5082-5093. ProLoc-GO >5locations humanandeukaryotes Huang,W.-L.,Tung,C.-W.,Ho,S.-W.,Hwang,S.-F.,&Ho,S.-Y. (2008) ProLoc-GO:utilizinginformativeGeneOntologytermsforsequence-basedpredictionofproteinsubcellularlocalization. BMCbioinformatics, 9,80. KnowPredsite >5locations prokaryotesandeukaryotes Lin,H.-N.,Chen,C.-T.,Sung,T.-Y.,Ho,S.-Y.,&Hsu,W.-L. (2009) Proteinsubcellularlocalizationpredictionofeukaryotesusingaknowledge-basedapproach. BMCbioinformatics, 10Suppl15,S8. MultiLoc2 >5locations animal,fungal,plant Blum,T,Briesemeister,S,andKohlbacher,O (2009) MultiLoc2:integratingphylogenyandGeneOntologytermsimprovessubcellularproteinlocalizationprediction. BMCBioinformatics, 10:274. PRED-SIGNAL signalpeptides archaea Bagos,PG,Tsirigos,K.D.,Plessas,S.K.,Liakopoulos,T.D.,&Hamodrakas,S.J. (2009) Predictionofsignalpeptidesinarchaea. Proteinengineering,design&selection:PEDS, 22(1),27-35. RSLPred chloroplast,cytoplasm,mitochondria,nucleus oryzasativaonly Kaundal,R.,&Raghava,G.P.S. (2009) RSLpred:anintegrativesystemforpredictingsubcellularlocalizationofriceproteinscombiningcompositionalandevolutionaryinformation. Proteomics, 9(9),2324-2342. SherLoc2 >5locations animal,fungi,plant Briesemeister,S.,Blum,T.,Brady,S.,Lam,Y.,Kohlbacher,O.,&Shatkay,H. (2009) SherLoc2:ahigh-accuracyhybridmethodforpredictingsubcellularlocalizationofproteins. Journalofproteomeresearch, 8(11),5363-5366. Cell-PLoc2.0 >5locations eukaryote,human,plant,virus,gram-positivebacteria,gram-negativebacteria Chou,K.andShen,H. (2010) Cell-PLoc2.0:animprovedpackageofweb-serversforpredictingsubcellularlocalizationofproteinsinvariousorganisms. NaturalScience, 2,1090-1103. CoBaltDB >5locations prokaryotes Goudenège,D.,Avner,S.,Lucchetti-Miganeh,C.,&Barloy-Hubler,F. (2010) CoBaltDB:Completebacterialandarchaealorfeomessubcellularlocalizationdatabaseandassociatedresources. BMCmicrobiology, 10,88. PSORTb >5locations gram-positiveandgram-negativebacteria Yu,N.Y.,Wagner,J.R.,Laird,M.R.,Melli,G.,Rey,S.,Lo,R.,...Brinkman,F.S.L. (2010) PSORTb3.0:improvedproteinsubcellularlocalizationpredictionwithrefinedlocalizationsubcategoriesandpredictivecapabilitiesforallprokaryotes. Bioinformatics(Oxford,England), 26(13),1608-1615. SCLPred cytoplasm,mitochondrion,nucleus,secretory,chloroplast animals,plants,fungi Mooney,C.,Wang,Y.-H.,&Pollastri,G. (2011) SCLpred:proteinsubcellularlocalizationpredictionbyN-to-1neuralnetworks. Bioinformatics(Oxford,England), 27(20),2812-2819. SignalP4.0 signalpeptide eukaryotic,gram-positivebacteria,gram-negativebacteria Petersen,T.N.,Brunak,S.,vonHeijne,G.,&Nielsen,H. (2011) SignalP4.0:discriminatingsignalpeptidesfromtransmembraneregions. Naturemethods, 8(10),785-786. SlocX >5locations aribdopsisthalianaonly Ryngajllo,M.,Childs,L.,Lohse,M.,Giorgi,F.M.,Lude,A.,Selbig,J.,&Usadel,B. (2011) SLocX:PredictingSubcellularLocalizationofArabidopsisProteinsLeveragingGeneExpressionData. Frontiersinplantscience, 2,43. APSLAP >5locations apoptosis Saravanan,V.,&Lakshmi,P.T.V. (2013) APSLAP:AnAdaptiveBoostingTechniqueforPredictingSubcellularLocalizationofApoptosisProtein. Actabiotheoretica, . IlocAnimal >5locations animal Lin,W.-Z.,Fang,J.-A.,Xiao,X.,&Chou,K.-C. (2013) iLoc-Animal:amulti-labellearningclassifierforpredictingsubcellularlocalizationofanimalproteins. MolecularbioSystems, 9(4),634-644.