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Volumn 60, Issue 2, 2005, Pages 275-280

Scoring docking models with evolutionary information

Author keywords

Blind test; CAPRI; Conserved regions; Correlated mutations; Interacting surface patches; Multiple sequence alignments; Protein docking; Tree determinants

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; CONFERENCE PAPER; EXPERIMENT; GENETIC CONSERVATION; MOLECULAR EVOLUTION; MOLECULAR MODEL; MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; SURFACE PROPERTY;

EID: 21644454183     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20570     Document Type: Conference Paper
Times cited : (40)

References (23)
  • 3
    • 0036601150 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein interactions
    • Valencia A, Pazos F. Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 2002;12:368-373.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 368-373
    • Valencia, A.1    Pazos, F.2
  • 4
    • 0037470597 scopus 로고    scopus 로고
    • Automatic methods for predicting functionally important residues
    • del Sol Mesa A, Pazos F, Valencia A. Automatic methods for predicting functionally important residues. J Mol Biol 2003;326: 1289-1302.
    • (2003) J Mol Biol , vol.326 , pp. 1289-1302
    • Del Sol Mesa, A.1    Pazos, F.2    Valencia, A.3
  • 5
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon A, Graur D, Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 2001;307:447-463.
    • (2001) J Mol Biol , vol.307 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 6
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari G, Sander C, Valencia A. A method to predict functional residues in proteins. Nat Struct Biol 1995;2:171-178.
    • (1995) Nat Struct Biol , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 7
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 2002;12:21-27.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 8
    • 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 DM, Philippi A, Sowa ME, Lichtarge O. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 2002;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
  • 9
    • 21644469836 scopus 로고    scopus 로고
    • Prediction of functional sites in proteins by evolutionary methods
    • Kamp RM, Calvete JJ, Choli-Papadopoulou, T, editors. Berlin/Heidelberg: Springer-Verlag
    • López-Romero P, Gómez MJ, Gómez-Puertas P, Valencia A. Prediction of functional sites in proteins by evolutionary methods. In: Kamp RM, Calvete JJ, Choli-Papadopoulou, T, editors. Methods in proteome and protein analysis. Berlin/Heidelberg: Springer-Verlag; 2004. p 319-336.
    • (2004) Methods in Proteome and Protein Analysis , pp. 319-336
    • López-Romero, P.1    Gómez, M.J.2    Gómez-Puertas, P.3    Valencia, A.4
  • 10
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18: 309-317.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Gobel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 11
    • 0030821675 scopus 로고    scopus 로고
    • Correlated mutations contain information about protein-protein interaction
    • Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997;271:511-523.
    • (1997) J Mol Biol , vol.271 , pp. 511-523
    • Pazos, F.1    Helmer-Citterich, M.2    Ausiello, G.3    Valencia, A.4
  • 13
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • Zhou HX, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001;44:336-343.
    • (2001) Proteins , vol.44 , pp. 336-343
    • Zhou, H.X.1    Shan, Y.2
  • 14
    • 0036122073 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites in heterocomplexes with neural networks
    • Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002;269:1356-1361.
    • (2002) Eur J Biochem , vol.269 , pp. 1356-1361
    • Fariselli, P.1    Pazos, F.2    Valencia, A.3    Casadio, R.4
  • 15
    • 13244292990 scopus 로고    scopus 로고
    • A two stage classifier for identification of protein-protein interface residues
    • Yan C, Dobbs D, Honavar V. A two stage classifier for identification of protein-protein interface residues. Bioinformatics 2004;20: 371-378.
    • (2004) Bioinformatics , vol.20 , pp. 371-378
    • Yan, C.1    Dobbs, D.2    Honavar, V.3
  • 16
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • Bradford JR, Westhead, DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005;21:1487-1494.
    • (2005) Bioinformatics , vol.21 , pp. 1487-1494
    • Bradford, J.R.1    Westhead, D.R.2
  • 18
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 19
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for multiple sequence alignments
    • Notredame C, Higgins D, Heringa J. T-Coffee: A novel method for multiple sequence alignments. J Mol Biol 2000;302:205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.2    Heringa, J.3
  • 20
    • 0041743084 scopus 로고    scopus 로고
    • Predicting reliable regions in protein alignments from sequence profiles
    • Tress ML, Jones DT, Valencia A. Predicting reliable regions in protein alignments from sequence profiles. J Mol Biol 2003;330: 705-718.
    • (2003) J Mol Biol , vol.330 , pp. 705-718
    • Tress, M.L.1    Jones, D.T.2    Valencia, A.3
  • 21
    • 2342421317 scopus 로고    scopus 로고
    • SQUARE - Determining reliable regions in sequence alignments
    • Tress ML, Graña O, Valencia A. SQUARE - determining reliable regions in sequence alignments. Bioinformatics 2004;20: 974-975.
    • (2004) Bioinformatics , vol.20 , pp. 974-975
    • Tress, M.L.1    Graña, O.2    Valencia, A.3
  • 22
    • 0031296607 scopus 로고    scopus 로고
    • Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
    • Vakser I. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins 1997;Suppl 1:226-230.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 226-230
    • Vakser, I.1
  • 23
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie DW, Kemp GJL. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.