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Volumn 31, Issue 13, 2003, Pages 3692-3697

SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; CELL NUCLEUS RECEPTOR; DNA BINDING PROTEIN; G PROTEIN COUPLED RECEPTOR; RNA BINDING PROTEIN; TYROSINE KINASE RECEPTOR; PROTEIN;

EID: 0042622243     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg600     Document Type: Article
Times cited : (535)

References (39)
  • 3
    • 0035252948 scopus 로고    scopus 로고
    • Computational methods for protein function analysis
    • Pellegrini,M. (2001) Computational methods for protein function analysis. Curr. Opin. Chem. Biol., 5, 46-50.
    • (2001) Curr. Opin. Chem. Biol. , vol.5 , pp. 46-50
    • Pellegrini, M.1
  • 5
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
    • Huynen,M., Snel,B., Lathe,W. and Bork,P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
    • (2000) Genome Res. , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe, W.3    Bork, P.4
  • 6
    • 0031897589 scopus 로고    scopus 로고
    • Predicting functions from protein sequences - Where are the bottlenecks?
    • Bork,P. and Koonin,E.V. (1998) Predicting functions from protein sequences - where are the bottlenecks? Nature Genet., 18, 313-318.
    • (1998) Nature Genet. , vol.18 , pp. 313-318
    • Bork, P.1    Koonin, E.V.2
  • 7
    • 0031626671 scopus 로고    scopus 로고
    • Practical aspects of multiple sequence alignment
    • Baxevanis,A.D. (1998) Practical aspects of multiple sequence alignment. Methods Biochem. Anal., 39, 172-188.
    • (1998) Methods Biochem. Anal. , vol.39 , pp. 172-188
    • Baxevanis, A.D.1
  • 8
    • 0031636531 scopus 로고    scopus 로고
    • Sequence alignment and database searching
    • Schuler,G.D. (1998) Sequence alignment and database searching. Methods Biochem. Anal., 39, 145-171.
    • (1998) Methods Biochem. Anal. , vol.39 , pp. 145-171
    • Schuler, G.D.1
  • 9
    • 0034040754 scopus 로고    scopus 로고
    • Functional inferences from reconstructed evolutionary biology involving rectified databases - An evolutionarily grounded approach to functional genomics
    • Benner,S.A., Chamberlin,S.G., Liberles,D.A., Govindarajan,S. and Knecht,L. (2000) Functional inferences from reconstructed evolutionary biology involving rectified databases - an evolutionarily grounded approach to functional genomics. Res. Microbiol., 151, 97-106.
    • (2000) Res. Microbiol. , vol.151 , pp. 97-106
    • Benner, S.A.1    Chamberlin, S.G.2    Liberles, D.A.3    Govindarajan, S.4    Knecht, L.5
  • 10
    • 0031976258 scopus 로고    scopus 로고
    • Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
    • Eisen,J.A. (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res., 8, 163-167.
    • (1998) Genome Res. , vol.8 , pp. 163-167
    • Eisen, J.A.1
  • 11
    • 0035367880 scopus 로고    scopus 로고
    • Determination of protein function, evolution and interactions by structural genomics
    • Teichmann,S.A., Murzin,A.G. and Chothia,C. (2001) Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Struct. Biol., 11, 354-363.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 354-363
    • Teichmann, S.A.1    Murzin, A.G.2    Chothia, C.3
  • 12
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 13
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright,A.J., Iliopoulos,I., Kyrpides,N. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.3    Ouzounis, C.A.4
  • 14
    • 0033828623 scopus 로고    scopus 로고
    • Guilt by association: Contextual information in genome analysis
    • Aravind,L. (2000) Guilt by association: contextual information in genome analysis. Genome Res., 10, 1074-1077.
    • (2000) Genome Res. , vol.10 , pp. 1074-1077
    • Aravind, L.1
  • 15
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock,J.R. and Gough,D.A. (2001) Predicting protein-protein interactions from primary structure. Bioinformatics, 17, 455-462.
    • (2001) Bioinformatics , vol.17 , pp. 455-462
    • Bock, J.R.1    Gough, D.A.2
  • 16
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright,A.J., Van Dongen,S.V. and Ouzounis,C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.V.2    Ouzounis, C.A.3
  • 17
    • 0033944826 scopus 로고    scopus 로고
    • GeneRage: A robust algorithm for sequence clustering and domain detection
    • Enright,A.J. and Ozounis,C.A. (2000) GeneRage: a robust algorithm for sequence clustering and domain detection. Bioinformatics, 16, 451-457.
    • (2000) Bioinformatics , vol.16 , pp. 451-457
    • Enright, A.J.1    Ozounis, C.A.2
  • 19
    • 0035292250 scopus 로고    scopus 로고
    • Issues in predicting protein function from sequence
    • Ponting,C.P. (2001) Issues in predicting protein function from sequence. Brief Bioinform., 2, 19-29.
    • (2001) Brief Bioinform. , vol.2 , pp. 19-29
    • Ponting, C.P.1
  • 20
  • 21
    • 0035170508 scopus 로고    scopus 로고
    • Collecting and harvesting biological data: The GPCRDB and NucleaRDB information systems
    • Horn,F., Vriend,G. and Cohen,F.E. (2001) Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res., 29, 346-349.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 346-349
    • Horn, F.1    Vriend, G.2    Cohen, F.E.3
  • 22
    • 0343603660 scopus 로고    scopus 로고
    • A functional-phylogenetic classification system for transmembrane solute transporters
    • Saier,M.H. Jr (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev., 64, 354-411.
    • (2000) Microbiol. Mol. Biol. Rev. , vol.64 , pp. 354-411
    • Saier Jr., M.H.1
  • 23
    • 0035172258 scopus 로고    scopus 로고
    • LGICdb: The ligand-gated ion channel database
    • Le Novere,N. and Changeux,J.-P. (2001) LGICdb: the ligand-gated ion channel database. Nucleic Acids Res., 29, 294-295.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 294-295
    • Le Novere, N.1    Changeux, J.-P.2
  • 24
    • 27144489164 scopus 로고    scopus 로고
    • A tutorial on Support Vector Machine for pattern recognition
    • Burges,C.J.C. (1998) A tutorial on Support Vector Machine for pattern recognition. Data Min. Knowl. Disc., 2, 121-167.
    • (1998) Data Min. Knowl. Disc. , vol.2 , pp. 121-167
    • Burges, C.J.C.1
  • 25
    • 0036166451 scopus 로고    scopus 로고
    • Classifying G-protein coupled receptors with support vector machines
    • Karchin,R., Karplus,K. and Haussler,D. (2002) Classifying G-protein coupled receptors with support vector machines. Bioinformatics, 18, 147-159.
    • (2002) Bioinformatics , vol.18 , pp. 147-159
    • Karchin, R.1    Karplus, K.2    Haussler, D.3
  • 26
    • 0042367635 scopus 로고    scopus 로고
    • Support Vector Machine classification of physical and biological datasets
    • In press
    • Cai,C.Z., Wang,W.L. and Chen,Y.Z. (2003) Support Vector Machine classification of physical and biological datasets. Inter. J. Mod. Phys. C., in press.
    • (2003) Inter. J. Mod. Phys. C.
    • Cai, C.Z.1    Wang, W.L.2    Chen, Y.Z.3
  • 27
    • 0035014847 scopus 로고    scopus 로고
    • Multi-class protein fold recognition using support vector machines and neural networks
    • Ding,C.H.Q. and Dubchak,I. (2001) Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics, 17, 349-358.
    • (2001) Bioinformatics , vol.17 , pp. 349-358
    • Ding, C.H.Q.1    Dubchak, I.2
  • 28
    • 0037103004 scopus 로고    scopus 로고
    • Prediction of protein solvent accessibility using support vector machines
    • Yuan,Z., Burrage,K. and Mattick,J.S. (2002) Prediction of protein solvent accessibility using support vector machines. Proteins, 48, 566-570.
    • (2002) Proteins , vol.48 , pp. 566-570
    • Yuan, Z.1    Burrage, K.2    Mattick, J.S.3
  • 29
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
    • Hua,S.J. and Sun,Z.R. (2001) A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. J. Mol. Biol., 308, 397-407.
    • (2001) J. Mol. Biol. , vol.308 , pp. 397-407
    • Hua, S.J.1    Sun, Z.R.2
  • 30
    • 0036007085 scopus 로고    scopus 로고
    • Prediction of protein structural classes by support vector machines
    • Cai,Y.D., Liu,X.J., Xu,X.B. and Chou,K.C. (2002) Prediction of protein structural classes by support vector machines. Comput. Chem., 26, 293-296.
    • (2002) Comput. Chem. , vol.26 , pp. 293-296
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 33
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • Dubchak,I., Muchnik,I., Holbrook,S.R. and Kim,S.-H. (1995) Prediction of protein folding class using global description of amino acid sequence. Proc. Natl Acad. Sci. USA, 92, 8700-8704.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.-H.4
  • 35
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: An overview
    • Baldi,P., Brunak,S., Chauvin,Y., Anderson,C.A.F. and Nielsen,H. (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics, 16, 412-419.
    • (2000) Bioinformatics , vol.16 , pp. 412-419
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Anderson, C.A.F.4    Nielsen, H.5
  • 36
    • 0035542934 scopus 로고    scopus 로고
    • The (betaalpha)(8) glycosidases: Sequence and structure analyses suggest distant evolutionary relationships
    • Nagano,N., Porter,C.T. and Thornton,J.M. (2001) The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships. Protein Eng., 14, 845-855.
    • (2001) Protein Eng. , vol.14 , pp. 845-855
    • Nagano, N.1    Porter, C.T.2    Thornton, J.M.3
  • 37
    • 0027070916 scopus 로고
    • Recognition of distantly related protein sequences using conserved motifs and neural networks
    • Frishman,D. and Argos,P. (1992) Recognition of distantly related protein sequences using conserved motifs and neural networks. J. Mol. Biol., 228, 951-962.
    • (1992) J. Mol. Biol. , vol.228 , pp. 951-962
    • Frishman, D.1    Argos, P.2
  • 38
    • 0033590164 scopus 로고    scopus 로고
    • Distantly related cousins of MAP kinase: Biochemical properties and possible physiological functions
    • Miyata,Y. and Nishida,E. (1999) Distantly related cousins of MAP kinase: biochemical properties and possible physiological functions. Biochem. Biophys. Res. Commun., 266, 291-295.
    • (1999) Biochem. Biophys. Res. Commun. , vol.266 , pp. 291-295
    • Miyata, Y.1    Nishida, E.2
  • 39
    • 0036948143 scopus 로고    scopus 로고
    • Structure-dependent sequence alignment for remotely related proteins
    • Yang,A.S. (2002) Structure-dependent sequence alignment for remotely related proteins. Bioinformatics, 18, 1658-1665.
    • (2002) Bioinformatics , vol.18 , pp. 1658-1665
    • Yang, A.S.1


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