Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction (original) (raw)
R Apweiler A Bairoch CH Wu WC Barker B Boeckmann S Ferro E Gasteiger H Huang R Lopez M Magrane MJ Martin DA Natale C O’Donovan N Redaschi LS Yeh (2004)ArticleTitleUniProt: the Universal Protein knowledgebase_Nucleic Acids Res_ 32 D115–D119Occurrence Handle14681372Occurrence Handle10.1093/nar/gkh131Occurrence Handle1:CAS:528:DC%2BD3sXhtVSru7vK ArticlePubMedCAS Google Scholar
M Ashburner CA Ball JA Blake D Botstein H Butler JM Cherry AP Davis K Dolinski SS Dwight JT Eppig MA Harris DP Hill L Issel-Tarver A Kasarskis S Lewis JC Matese JE Richardson M Ringwald GM Rubin G Sherlock (2000)ArticleTitleGene ontology: tool for the unification of biology_Nature Genet_ 25 25–29Occurrence Handle10802651Occurrence Handle10.1038/75556Occurrence Handle1:CAS:528:DC%2BD3cXjtFSlsbc%3D ArticlePubMedCAS Google Scholar
A Bairoch R Apweiler (2000)ArticleTitleThe SWISS-PROT protein sequence data bank and its supplement TrEMBL_Nucleic Acids Res_ 25 31–36Occurrence Handle10.1093/nar/25.1.31 Article Google Scholar
E Camon M Magrane D Barrell V Lee E Dimmer J Maslen D Binns N Harte R Lopez R Apweiler (2004)ArticleTitleThe Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology_Nucleic Acids Res_ 32 D262–D266Occurrence Handle14681408Occurrence Handle10.1093/nar/gkh021Occurrence Handle1:CAS:528:DC%2BD3sXhtVSrur%2FM ArticlePubMedCAS Google Scholar
Y Cao S Liu L Zhang J Qin J Wang K Tang (2006)ArticleTitlePrediction of protein structural class with Rough Sets_BMC Bioinformatics_ 7 20Occurrence Handle16412240Occurrence Handle10.1186/1471-2105-7-20Occurrence Handle1:CAS:528:DC%2BD28Xht1Sks7s%3D ArticlePubMedCAS Google Scholar
J Cedano P Aloy JA P’erez-Pons E Querol (1997)ArticleTitleRelation between amino acid composition and cellular location of proteins_J Mol Biol_ 266 594–600Occurrence Handle9067612Occurrence Handle10.1006/jmbi.1996.0804Occurrence Handle1:CAS:528:DyaK2sXhslKksL4%3D ArticlePubMedCAS Google Scholar
C Chen X Zhou Y Tian X Zou P Cai (2006)ArticleTitlePredicting protein structural class with pseudo-amino acid composition and support vector machine fusion network_Anal Biochem_ 357 116–121Occurrence Handle16920060Occurrence Handle10.1016/j.ab.2006.07.022Occurrence Handle1:CAS:528:DC%2BD28XpsVOgs78%3D ArticlePubMedCAS Google Scholar
KC Chou (1995)ArticleTitleA novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space_Proteins Struct Funct Genet_ 21 319–344Occurrence Handle7567954Occurrence Handle10.1002/prot.340210406Occurrence Handle1:CAS:528:DyaK2MXls12rsb0%3D ArticlePubMedCAS Google Scholar
KC Chou (2000a)ArticleTitleReview: prediction of protein structural classes and subcellular locations_Curr Protein Peptide Sci_ 1 171–208Occurrence Handle10.2174/1389203003381379Occurrence Handle1:CAS:528:DC%2BD3cXnsVeisL0%3D ArticleCAS Google Scholar
KC Chou (2000b)ArticleTitleReview: prediction of tight turns and their types in proteins_Anal Biochem_ 286 1–16Occurrence Handle10.1006/abio.2000.4757Occurrence Handle1:CAS:528:DC%2BD3cXntlKrsL0%3D ArticleCAS Google Scholar
KC Chou (2001)ArticleTitlePrediction of protein cellular attributes using pseudo amino acid composition_Proteins Struct Funct Genet_ 43 246–255Occurrence Handle11288174Occurrence Handle10.1002/prot.1035Occurrence Handle1:CAS:528:DC%2BD3MXjtFOls74%3D ArticlePubMedCAS Google Scholar
KC Chou (2004)ArticleTitleReview: structural bioinformatics and its impact to biomedical science_Curr Med Chem_ 11 2105–2134Occurrence Handle15279552Occurrence Handle1:CAS:528:DC%2BD2cXlslWltbw%3D PubMedCAS Google Scholar
KC Chou YD Cai (2002)ArticleTitleUsing functional domain composition and support vector machines for prediction of protein subcellular location_J Biol Chem_ 277 45765–45769Occurrence Handle12186861Occurrence Handle10.1074/jbc.M204161200Occurrence Handle1:CAS:528:DC%2BD38XovFKjurg%3D ArticlePubMedCAS Google Scholar
KC Chou YD Cai (2003)ArticleTitleA new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology_Biochem Biophys Res Commun_ 311 743–747Occurrence Handle14623335Occurrence Handle10.1016/j.bbrc.2003.10.062Occurrence Handle1:CAS:528:DC%2BD3sXos12lurs%3D ArticlePubMedCAS Google Scholar
KC Chou YD Cai (2004)ArticleTitlePrediction of protein subcellular locations by GO-FunD-PseAA predictor_Biochem Biophys Res Commun_ 320 1236–1239Occurrence Handle15249222Occurrence Handle10.1016/j.bbrc.2004.06.073Occurrence Handle1:CAS:528:DC%2BD2cXls1eisL0%3D ArticlePubMedCAS Google Scholar
KC Chou YD Cai (2005)ArticleTitlePrediction of membrane protein types by incorporating amphipathic effects_J Chem Inform Model_ 45 407–413Occurrence Handle10.1021/ci049686vOccurrence Handle1:CAS:528:DC%2BD2MXht1aqtLs%3D ArticleCAS Google Scholar
KC Chou HB Shen (2006)ArticleTitlePredicting protein subcellular location by fusing multiple classifiers_J Cell Biochem_ 99 517–527Occurrence Handle16639720Occurrence Handle10.1002/jcb.20879Occurrence Handle1:CAS:528:DC%2BD28XhtVSktL3J ArticlePubMedCAS Google Scholar
KC Chou CT Zhang (1994)ArticleTitlePredicting protein folding types by distance functions that make allowances for amino acid interactions_J Biol Chem_ 269 22014–22020Occurrence Handle8071322Occurrence Handle1:CAS:528:DyaK2cXlslCls7o%3D PubMedCAS Google Scholar
KC Chou CT Zhang (1995)ArticleTitleReview: prediction of protein structural classes_Crit Rev Biochem Mol Biol_ 30 275–349Occurrence Handle7587280Occurrence Handle1:CAS:528:DyaK2MXosFentb8%3D PubMedCAS Google Scholar
KC Chou CT Zhang GM Maggiora (1997)ArticleTitleDisposition of amphiphilic helices in heteropolar environments_Proteins Struct Funct Genet_ 28 99–108Occurrence Handle9144795Occurrence Handle10.1002/(SICI)1097-0134(199705)28:1<99::AID-PROT10>3.0.CO;2-COccurrence Handle1:CAS:528:DyaK2sXjtVKltrY%3D ArticlePubMedCAS Google Scholar
TM Cover PE Hart (1967)ArticleTitleNearest neighbour pattern classification_IEEE Trans Inform Theory_ IT-13 21–27Occurrence Handle10.1109/TIT.1967.1053964 Article Google Scholar
T Denoeux (1995)ArticleTitleA k-nearest neighbor classification rule based on Dempster-Shafer theory_IEEE Trans Systems Man Cybern_ 25 804–813Occurrence Handle10.1109/21.376493 Article Google Scholar
QS Du ZQ Jiang WZ He DP Li KC Chou (2006)ArticleTitleAmino acid principal component analysis (AAPCA) and its applications in protein structural class prediction_J Biomol Struct Dyn_ 23 635–640Occurrence Handle16615809Occurrence Handle1:CAS:528:DC%2BD28XkvVCntLw%3D PubMedCAS Google Scholar
ZP Feng (2001)ArticleTitlePrediction of the subcellular location of prokaryotic proteins based on a new representation of the amino acid composition_Biopolymers_ 58 491–499Occurrence Handle11241220Occurrence Handle10.1002/1097-0282(20010415)58:5<491::AID-BIP1024>3.0.CO;2-IOccurrence Handle1:CAS:528:DC%2BD3MXisVSntb8%3D ArticlePubMedCAS Google Scholar
ZP Feng (2002)ArticleTitleAn overview on predicting the subcellular location of a protein_In Silico Biol_ 2 291–303Occurrence Handle12542414Occurrence Handle1:CAS:528:DC%2BD38Xpsl2lu7k%3D PubMedCAS Google Scholar
QB Gao ZZ Wang C Yan YH Du (2005a)ArticleTitlePrediction of protein subcellular location using a combined feature of sequence_FEBS Lett_ 579 3444–3448Occurrence Handle10.1016/j.febslet.2005.05.021Occurrence Handle1:CAS:528:DC%2BD2MXlt1KjsL0%3D ArticleCAS Google Scholar
Y Gao SH Shao X Xiao YS Ding YS Huang ZD Huang KC Chou (2005b)ArticleTitleUsing pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter_Amino Acids_ 28 373–376Occurrence Handle10.1007/s00726-005-0206-9Occurrence Handle1:CAS:528:DC%2BD2MXlt1Kmurw%3D ArticleCAS Google Scholar
A Garg M Bhasin GP Raghava (2005)ArticleTitleSupport vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search_J Biol Chem_ 280 14427–14432Occurrence Handle15647269Occurrence Handle10.1074/jbc.M411789200Occurrence Handle1:CAS:528:DC%2BD2MXjtFSmt7g%3D ArticlePubMedCAS Google Scholar
J Guo Y Lin X Liu (2006a)ArticleTitleGNBSL: a new integrative system to predict the subcellular location for Gram-negative bacteria proteins_Proteomics_ 6 5099–5105Occurrence Handle10.1002/pmic.200600064Occurrence Handle1:CAS:528:DC%2BD28XhtFarsbzO ArticleCAS Google Scholar
YZ Guo M Li M Lu Z Wen K Wang G Li J Wu (2006b)ArticleTitleClassifying G protein-coupled receptors and nuclear receptors based on protein power spectrum from fast Fourier transform_Amino Acids_ 30 397–402Occurrence Handle10.1007/s00726-006-0332-zOccurrence Handle1:CAS:528:DC%2BD28Xls1egs7o%3D ArticleCAS Google Scholar
A Hoglund P Donnes T Blum HW Adolph O Kohlbacher (2006)ArticleTitleMultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition_Bioinformatics_ 22 1158–1165Occurrence Handle16428265Occurrence Handle10.1093/bioinformatics/btl002Occurrence Handle1:CAS:528:DC%2BD28Xktlaku78%3D ArticlePubMedCAS Google Scholar
JM Keller MR Gray JA Givens (1985)ArticleTitleA fuzzy k-nearest neighbours algorithm_IEEE Trans Syst Man Cybern_ 15 580–585 Google Scholar
V Lee E Camon E Dimmer D Barrell R Apweiler (2005)ArticleTitleWho tangos with GOA?-Use of Gene Ontology Annotation (GOA) for biological interpretation of ‘-omics’ data and for validation of automatic annotation tools_In Silico Biol_ 5 5–8Occurrence Handle15972001Occurrence Handle1:CAS:528:DC%2BD2MXksVejtrk%3D PubMedCAS Google Scholar
H Liu M Wang KC Chou (2005a)ArticleTitleLow-frequency Fourier spectrum for predicting membrane protein types_Biochem Biophys Res Commun_ 336 737–739Occurrence Handle10.1016/j.bbrc.2005.08.160Occurrence Handle1:CAS:528:DC%2BD2MXhtVegtLfP ArticleCAS Google Scholar
H Liu J Yang JG Ling KC Chou (2005b)ArticleTitlePrediction of protein signal sequences and their cleavage sites by statistical rulers_Biochem Biophys Res Commun_ 338 1005–1011Occurrence Handle10.1016/j.bbrc.2005.10.046Occurrence Handle1:CAS:528:DC%2BD2MXht1Wjur3F ArticleCAS Google Scholar
G Lubec L Afjehi-Sadat JW Yang JP John (2005)ArticleTitleSearching for hypothetical proteins: theory and practice based upon original data and literature_Prog Neurobiol_ 77 90–127Occurrence Handle16271823Occurrence Handle10.1016/j.pneurobio.2005.10.001Occurrence Handle1:CAS:528:DC%2BD2MXht1GhtbvK ArticlePubMedCAS Google Scholar
RY Luo ZP Feng JK Liu (2002)ArticleTitlePrediction of protein strctural class by amino acid and polypeptide composition_Eur J Biochem_ 269 4219–4225Occurrence Handle12199700Occurrence Handle10.1046/j.1432-1033.2002.03115.xOccurrence Handle1:CAS:528:DC%2BD38Xnt1eiur8%3D ArticlePubMedCAS Google Scholar
PC Mahalanobis (1936)ArticleTitleOn the generalized distance in statistics_Proc Natl Inst Sci India_ 2 49–55 Google Scholar
Mardia KV, Kent JT, Bibby JM (1979) Multivariate analysis chapter 11: Discriminant analysis; chapter 12: Multivariate analysis of variance; chapter 13: Cluster analysis. Academic Press, London pp 322–381
S Matsuda JP Vert H Saigo N Ueda H Toh T Akutsu (2005)ArticleTitleA novel representation of protein sequences for prediction of subcellular location using support vector machines_Protein Sci_ 14 2804–2813Occurrence Handle16251364Occurrence Handle10.1110/ps.051597405Occurrence Handle1:CAS:528:DC%2BD2MXhtF2it77K ArticlePubMedCAS Google Scholar
BW Matthews (1975)ArticleTitleComparison of the predicted and observed secondary structure of T4 phage lysozyme_Biochim Biophys Acta_ 405 442–451Occurrence Handle1180967Occurrence Handle1:CAS:528:DyaE2MXlslCksbk%3D PubMedCAS Google Scholar
K Nakai (2000)ArticleTitleProtein sorting signals and prediction of subcellular localization_Adv Protein Chem_ 54 277–344Occurrence Handle10829231Occurrence Handle1:CAS:528:DC%2BD3cXltFSqs70%3DOccurrence Handle10.1016/S0065-3233(00)54009-1 ArticlePubMedCAS Google Scholar
K Nakai P Horton (1999)ArticleTitlePSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization_Trends Biochem Sci_ 24 34–36Occurrence Handle10087920Occurrence Handle10.1016/S0968-0004(98)01336-XOccurrence Handle1:CAS:528:DyaK1MXks12qtLk%3D ArticlePubMedCAS Google Scholar
H Nakashima K Nishikawa (1994)ArticleTitleDiscrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies_J Mol Biol_ 238 54–61Occurrence Handle8145256Occurrence Handle10.1006/jmbi.1994.1267Occurrence Handle1:CAS:528:DyaK2cXivFemtrw%3D ArticlePubMedCAS Google Scholar
H Nakashima K Nishikawa T Ooi (1986)ArticleTitleThe folding type of a protein is relevant to the amino acid composition_J Biochem_ 99 152–162 Google Scholar
KJ Park M Kanehisa (2003)ArticleTitlePrediction of protein subcellular locations by support vector machines using compositions of amino acid and amino acid pairs_Bioinformatics_ 19 1656–1663Occurrence Handle12967962Occurrence Handle10.1093/bioinformatics/btg222Occurrence Handle1:CAS:528:DC%2BD3sXnt1Gqu78%3D ArticlePubMedCAS Google Scholar
KCS Pillai (1985) Mahalanobis D2 S Kotz NL Johnson (Eds) Encyclopedia of statistical sciencesNumberInSeries5 Wiley New York 176–181 Google Scholar
T Radford (2003)ArticleTitleMetaphors and dreams_The Scientist_ 17 24–26 Google Scholar
A Reinhardt T Hubbard (1998)ArticleTitleUsing neural networks for prediction of the subcellular location of proteins_Nucleic Acids Res_ 26 2230–2236Occurrence Handle9547285Occurrence Handle10.1093/nar/26.9.2230Occurrence Handle1:CAS:528:DyaK1cXjtFylsLw%3D ArticlePubMedCAS Google Scholar
HB Shen KC Chou (2005)ArticleTitleUsing optimized evidence-theoretic K-nearest neighbor classifier and pseudo amino acid composition to predict membrane protein types_Biochem Biophys Res Commun_ 334 288–292Occurrence Handle16002049Occurrence Handle10.1016/j.bbrc.2005.06.087Occurrence Handle1:CAS:528:DC%2BD2MXmt1aqsLw%3D ArticlePubMedCAS Google Scholar
HB Shen J Yang KC Chou (2006)ArticleTitleFuzzy KNN for predicting membrane protein types from pseudo amino acid composition_J Theor Biol_ 240 9–13Occurrence Handle16197963Occurrence Handle10.1016/j.jtbi.2005.08.016Occurrence Handle1:CAS:528:DC%2BD28Xjs1Knt70%3D ArticlePubMedCAS Google Scholar
HB Shen J Yang XJ Liu KC Chou (2005)ArticleTitleUsing supervised fuzzy clustering to predict protein structural classes_Biochem Biophys Res Commun_ 334 577–581Occurrence Handle16023077Occurrence Handle10.1016/j.bbrc.2005.06.128Occurrence Handle1:CAS:528:DC%2BD2MXmsVOgurg%3D ArticlePubMedCAS Google Scholar
XD Sun RB Huang (2006)ArticleTitlePrediction of protein structural classes using support vector machines_Amino Acids_ 30 469–475Occurrence Handle16622605Occurrence Handle10.1007/s00726-005-0239-0Occurrence Handle1:CAS:528:DC%2BD28Xls1ehu7c%3D ArticlePubMedCAS Google Scholar
GL Wang RL DunbrackSuffixJr (2003)ArticleTitlePISCES: a protein sequence culling server_Bioinformatics_ 19 1589–1591Occurrence Handle12912846Occurrence Handle10.1093/bioinformatics/btg224Occurrence Handle1:CAS:528:DC%2BD3sXntlKmsLo%3D ArticlePubMedCAS Google Scholar
M Wang J Yang KC Chou (2005a)ArticleTitleUsing string kernel to predict signal peptide cleavage site based on subsite coupling model_Amino Acids_ 28 395–402Occurrence Handle10.1007/s00726-005-0189-6Occurrence Handle1:CAS:528:DC%2BD2MXlt1KmtbY%3D ArticleCAS Google Scholar
M Wang J Yang GP Liu ZJ Xu KC Chou (2004)ArticleTitleWeighted-support vector machines for predicting membrane protein types based on pseudo amino acid composition_Protein Eng Des Select_ 17 509–516Occurrence Handle10.1093/protein/gzh061Occurrence Handle1:CAS:528:DC%2BD2cXos1GisLY%3D ArticleCAS Google Scholar
M Wang J Yang ZJ Xu KC Chou (2005b)ArticleTitleSLLE for predicting membrane protein types_J Theor Biol_ 232 7–15Occurrence Handle10.1016/j.jtbi.2004.07.023Occurrence Handle1:CAS:528:DC%2BD2cXovVKkur4%3D ArticleCAS Google Scholar
SQ Wang J Yang KC Chou (2006)ArticleTitleUsing stacked generalization to predict membrane protein types based on pseudo amino acid composition_J Theor Biol_ 242 941–946Occurrence Handle16806277Occurrence Handle10.1016/j.jtbi.2006.05.006Occurrence Handle1:CAS:528:DC%2BD28Xps1Oku70%3D ArticlePubMedCAS Google Scholar
Wen Z, Li M, Li Y, Guo Y, Wang K (2007) Delaunay triangulation with partial least squares projection to latent structures: a model for G-protein coupled receptors classification and fast structure recognition. Amino Acids (in press) (DOI: 10.1007/s00726-006-0341-y)
X Xiao S Shao Y Ding Z Huang Y Huang KC Chou (2005)ArticleTitleUsing complexity measure factor to predict protein subcellular location_Amino Acids_ 28 57–61Occurrence Handle15611847Occurrence Handle10.1007/s00726-004-0148-7Occurrence Handle1:CAS:528:DC%2BD2MXhsVKqsro%3D ArticlePubMedCAS Google Scholar
X Xiao SH Shao YS Ding ZD Huang KC Chou (2006a)ArticleTitleUsing cellular automata images and pseudo amino acid composition to predict protein sub-cellular location_Amino Acids_ 30 49–54Occurrence Handle10.1007/s00726-005-0225-6Occurrence Handle1:CAS:528:DC%2BD28XhsFCksrk%3D ArticleCAS Google Scholar
X Xiao SH Shao ZD Huang KC Chou (2006b)ArticleTitleUsing pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor_J Comput Chem_ 27 478–482Occurrence Handle10.1002/jcc.20354Occurrence Handle1:CAS:528:DC%2BD28XitFyqsr4%3D ArticleCAS Google Scholar
SW Zhang Q Pan HC Zhang ZC Shao JY Shi (2006)ArticleTitlePrediction protein homo-oligomer types by pseudo amino acid composition: approached with an improved feature extraction and naive Bayes feature fusion_Amino Acids_ 30 461–468Occurrence Handle16773245Occurrence Handle10.1007/s00726-006-0263-8Occurrence Handle1:CAS:528:DC%2BD28Xls1egsr0%3D ArticlePubMedCAS Google Scholar
GP Zhou (1998)ArticleTitleAn intriguing controversy over protein structural class prediction_J Prot Chem_ 17 729–738Occurrence Handle10.1023/A:1020713915365Occurrence Handle1:CAS:528:DyaK1MXnslaltw%3D%3D ArticleCAS Google Scholar
GP Zhou N Assa-Munt (2001)ArticleTitleSome insights into protein structural class prediction_Proteins Struct Funct Genet_ 44 57–59Occurrence Handle11354006Occurrence Handle10.1002/prot.1071Occurrence Handle1:CAS:528:DC%2BD3MXktlSnsbk%3D ArticlePubMedCAS Google Scholar
GP Zhou K Doctor (2003)ArticleTitleSubcellular location prediction of apoptosis proteins_Proteins Struct Funct Genet_ 50 44–48Occurrence Handle12471598Occurrence Handle10.1002/prot.10251Occurrence Handle1:CAS:528:DC%2BD3sXlsVKmug%3D%3D ArticlePubMedCAS Google Scholar