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Volumn 34, Issue 13, 2006, Pages 3698-3707

Protein binding site prediction using an empirical scoring function

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; AMINO ACID; MULTIPROTEIN COMPLEX;

EID: 33747150197     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl454     Document Type: Article
Times cited : (215)

References (45)
  • 2
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: Modelling protein interactions
    • Aloy,P. and Russell,R.B. (2006) Structural systems biology: Modelling protein interactions. Nature Rev. Mol. Cell. Biol., 7, 188-197.
    • (2006) Nature Rev. Mol. Cell. Biol. , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 3
    • 1842861590 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
    • Wodak,S.J. and Mendez,R. (2004) Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications. Curr. Opin. Struct. Biol., 14, 242-249.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 242-249
    • Wodak, S.J.1    Mendez, R.2
  • 4
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Mendez,R., Leplae,R., De Maria,L. and Wodak,S.J. (2003) Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins, 52, 51-67.
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 5
    • 2642524483 scopus 로고    scopus 로고
    • A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
    • Liu,S., Zhang,C., Zhou,H. and Zhou,Y. (2004) A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins, 56, 93-101.
    • (2004) Proteins , vol.56 , pp. 93-101
    • Liu, S.1    Zhang, C.2    Zhou, H.3    Zhou, Y.4
  • 6
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy,P., Querol,E., Aviles,F.X. and Sternberg,M.J. (2001) Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311, 395-408.
    • (2001) J. Mol. Biol. , vol.311 , pp. 395-408
    • Aloy, P.1    Querol, E.2    Aviles, F.X.3    Sternberg, M.J.4
  • 8
    • 21644446565 scopus 로고    scopus 로고
    • Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
    • Zhang,C., Liu,S. and Zhou,Y. (2005) Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins, 60, 314-318.
    • (2005) Proteins , vol.60 , pp. 314-318
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 9
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones,S. and Thornton,J.M. (1997) Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol., 272, 133-143.
    • (1997) J. Mol. Biol. , vol.272 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 10
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: A structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth,H., Raz,R. and Schreiber,G. (2004) ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol., 338, 181-199.
    • (2004) J. Mol. Biol. , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 11
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • Glaser,F., Steinberg,D.M., Vakser,I.A. and Ben-Tal,N. (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins, 43, 89-102.
    • (2001) Proteins , vol.43 , pp. 89-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 12
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young,L., Jernigan,R.L. and Covell,D.G. (1994) A role for surface hydrophobicity in protein-protein recognition. Protein Sci., 3,717-729.
    • (1994) Protein Sci. , vol.3 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 13
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte,L., Chothia,C. and Janin,J. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol., 285, 2177-2198.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 14
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones,S. and Thornton,J.M. (1996) Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 15
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • Zhou,H.X. and Shan,Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343.
    • (2001) Proteins , vol.44 , pp. 336-343
    • Zhou, H.X.1    Shan, Y.2
  • 16
    • 0036122073 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites in heterocomplexes with neural networks
    • Fariselli,P., Pazos,F., Valencia,A. and Casadio,R. (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem., 269, 1356-1361.
    • (2002) Eur. J. Biochem. , vol.269 , pp. 1356-1361
    • Fariselli, P.1    Pazos, F.2    Valencia, A.3    Casadio, R.4
  • 17
    • 1842454912 scopus 로고    scopus 로고
    • Prediction of functional sites by analysis of sequence and structure conservation
    • Panchenko,A.R., Kondrashov,F. and Bryant,S. (2004) Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci., 13, 884-892.
    • (2004) Protein Sci. , vol.13 , pp. 884-892
    • Panchenko, A.R.1    Kondrashov, F.2    Bryant, S.3
  • 18
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko,T., Bell,R.E., Mayrose,I., Glaser,F. and Ben-Tal,N. (2002) Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18, S71-S77.
    • (2002) Bioinformatics , vol.18
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 19
    • 31944439550 scopus 로고    scopus 로고
    • Exploiting sequence and structure homologs to identify protein-protein binding sites
    • Chung,J.L., Wang,W. and Bourne,P.E. (2006) Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins, 62, 630-640.
    • (2006) Proteins , vol.62 , pp. 630-640
    • Chung, J.L.1    Wang, W.2    Bourne, P.E.3
  • 20
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot spots at protein interfaces
    • Hu,Z., Ma,B., Wolfson,H. and Nussinov,R. (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins, 39, 331-342.
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 21
    • 0042010066 scopus 로고    scopus 로고
    • Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem
    • Bradford,J.R. and Westhead,D.R. (2003) Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem. Protein Sci., 12, 2099-2103.
    • (2003) Protein Sci. , vol.12 , pp. 2099-2103
    • Bradford, J.R.1    Westhead, D.R.2
  • 22
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • Caffrey,D.R., Somaroo,S., Hughes,J.D., Mintseris,J. and Huang,E.S. (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci., 13, 190-202.
    • (2004) Protein Sci. , vol.13 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5
  • 23
    • 0028566271 scopus 로고
    • The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences
    • Grishin,N.V. and Phillips,M.A. (1994) The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences. Protein Sci., 3, 2455-2458.
    • (1994) Protein Sci. , vol.3 , pp. 2455-2458
    • Grishin, N.V.1    Phillips, M.A.2
  • 24
    • 23344451687 scopus 로고    scopus 로고
    • Structure, function, and evolution of transient and obligate protein-protein interactions
    • Mintseris,J. and Weng,Z. (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl Acad. Sci. USA, 102, 10930-10935.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 10930-10935
    • Mintseris, J.1    Weng, Z.2
  • 25
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge,O., Bourne,H.R. and Cohen,F.E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358.
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 26
    • 0036300444 scopus 로고    scopus 로고
    • Structural clusters of evolutionary trace residues are statistically significant and common in proteins
    • Madabushi,S., Yao,H., Marsh,M., Kristensen,D.M., Philippi,A., Sowa,M.E. and Lichtarge,O. (2002) Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J. Mol. Biol., 316, 139-154.
    • (2002) J. Mol. Biol. , vol.316 , pp. 139-154
    • Madabushi, S.1    Yao, H.2    Marsh, M.3    Kristensen, D.M.4    Philippi, A.5    Sowa, M.E.6    Lichtarge, O.7
  • 27
    • 0026055156 scopus 로고
    • Analysis of the steric strain in the polypeptide backbone of protein molecules
    • Herzberg,O. and Moult,J. (1991) Analysis of the steric strain in the polypeptide backbone of protein molecules. Proteins, 11, 223-229.
    • (1991) Proteins , vol.11 , pp. 223-229
    • Herzberg, O.1    Moult, J.2
  • 28
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock,A.H. (2001) Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol., 312, 885-896.
    • (2001) J. Mol. Biol. , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 29
    • 0344405703 scopus 로고    scopus 로고
    • Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation
    • Ota,M., Kinoshita,K. and Nishikawa,K. (2003) Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J. Mol. Biol., 327, 1053-1064.
    • (2003) J. Mol. Biol. , vol.327 , pp. 1053-1064
    • Ota, M.1    Kinoshita, K.2    Nishikawa, K.3
  • 30
    • 4544230537 scopus 로고    scopus 로고
    • Distinguishing structural and functional restraints in evolution in order to identify interaction sites
    • Chelliah,V., Chen,L., Blundell,T.L. and Lovell,S.C. (2004) Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J. Mol. Biol., 342, 1487-1504.
    • (2004) J. Mol. Biol , vol.342 , pp. 1487-1504
    • Chelliah, V.1    Chen, L.2    Blundell, T.L.3    Lovell, S.C.4
  • 31
    • 27144551715 scopus 로고    scopus 로고
    • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
    • Cheng,G., Qian,B., Samudrala,R. and Baker,D. (2005) Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res., 33, 5861-5867.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 5861-5867
    • Cheng, G.1    Qian, B.2    Samudrala, R.3    Baker, D.4
  • 32
    • 0031565729 scopus 로고    scopus 로고
    • Analysis of protein-protein interaction sites using surface patches
    • Jones,S. and Thornton,J.M. (1997) Analysis of protein-protein interaction sites using surface patches. J. Mol. Biol., 272, 121-132.
    • (1997) J. Mol. Biol. , vol.272 , pp. 121-132
    • Jones, S.1    Thornton, J.M.2
  • 33
    • 0036893020 scopus 로고    scopus 로고
    • Side-chain conformational entropy at protein-protein interfaces
    • Cole,C. and Warwicker,J. (2002) Side-chain conformational entropy at protein-protein interfaces. Protein Sci., 11, 2860-2870.
    • (2002) Protein Sci. , vol.11 , pp. 2860-2870
    • Cole, C.1    Warwicker, J.2
  • 34
    • 0037422589 scopus 로고    scopus 로고
    • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
    • Fernandez,A. and Scheraga,H.A. (2003) Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl Acad. Sci. USA, 100, 113-118.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 113-118
    • Fernandez, A.1    Scheraga, H.A.2
  • 35
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • Bradford,J.R. and Westhead,D.R. (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics, 21, 1487-1494.
    • (2005) Bioinformatics , vol.21 , pp. 1487-1494
    • Bradford, J.R.1    Westhead, D.R.2
  • 36
    • 23044487169 scopus 로고    scopus 로고
    • Statistical analysis and prediction of protein-protein interfaces
    • Bordner,A.J. and Abagyan,R. (2005) Statistical analysis and prediction of protein-protein interfaces. Proteins, 60, 353-366.
    • (2005) Proteins , vol.60 , pp. 353-366
    • Bordner, A.J.1    Abagyan, R.2
  • 37
    • 24344484686 scopus 로고    scopus 로고
    • Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data
    • Chen,H. and Zhou,H.X. (2005) Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data. Proteins, 61, 21-35.
    • (2005) Proteins , vol.61 , pp. 21-35
    • Chen, H.1    Zhou, H.X.2
  • 38
    • 6344291590 scopus 로고    scopus 로고
    • Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores
    • Liang,S., Zhang,J., Zhang,S. and Guo,H. (2004) Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores. Proteins, 57, 548-557.
    • (2004) Proteins , vol.57 , pp. 548-557
    • Liang, S.1    Zhang, J.2    Zhang, S.3    Guo, H.4
  • 39
    • 0347089142 scopus 로고    scopus 로고
    • Effective scoring function for protein sequence design
    • Liang,S. and Grishin,N.V. (2004) Effective scoring function for protein sequence design. Proteins, 54, 271-281.
    • (2004) Proteins , vol.54 , pp. 271-281
    • Liang, S.1    Grishin, N.V.2
  • 40
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack,R.L.,Jr and Cohen,F.E. (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci., 6, 1661-1681.
    • (1997) Protein Sci. , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 41
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 44
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word,J.M., Lovell,S.C., Richardson,J.S. and Richardson,D.C. (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol., 285, 1735-1747.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 45
    • 0038187615 scopus 로고    scopus 로고
    • A protein-protein docking benchmark
    • Chen,R., Mintseris,J., Janin,J. and Weng,Z. (2003) A protein-protein docking benchmark. Proteins, 52, 88-91.
    • (2003) Proteins , vol.52 , pp. 88-91
    • Chen, R.1    Mintseris, J.2    Janin, J.3    Weng, Z.4


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