메뉴 건너뛰기




Volumn 13, Issue 4, 2004, Pages 884-892

Prediction of functional sites by analysis of sequence and structure conservation

Author keywords

Evolutionary conservation; Prediction of functional residues; Protein domains

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; EVOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 1842454912     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03465504     Document Type: Article
Times cited : (118)

References (34)
  • 1
    • 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
  • 3
    • 0031157904 scopus 로고    scopus 로고
    • Classification of protein families and detection of the determinant residues with an improved self-organizing map
    • Andrade, M.A., Casari, G., Sander, C., and Valencia, A. 1997. Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biol. Cybern. 76: 441-450.
    • (1997) Biol. Cybern. , vol.76 , pp. 441-450
    • Andrade, M.A.1    Casari, G.2    Sander, C.3    Valencia, A.4
  • 5
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari, G., Sander, C., and Valencia, A. 1995. A method to predict functional residues in proteins. Nat. Struct. Biol. 2: 171-178.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 7
    • 0037470597 scopus 로고    scopus 로고
    • Automatic methods for predicting functionally important residues
    • del Sol Mesa, A., Pazos, F., and Valencia, A. 2003. Automatic methods for predicting functionally important residues. J. Mol. Biol. 326: 1289-1302.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1289-1302
    • Del Sol Mesa, A.1    Pazos, F.2    Valencia, A.3
  • 8
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • Devos, D. and Valencia, A. 2000. Practical limits of function prediction. Proteins 41: 98-107.
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 9
    • 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
  • 10
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny inference package
    • Felsenstein, J. 1989. PHYLIP-Phylogeny inference package. Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 11
    • 0001969211 scopus 로고    scopus 로고
    • Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
    • Gribskov, M. and Robinson, N.L. 1996. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem. 20: 25-33.
    • (1996) Comput. Chem. , vol.20 , pp. 25-33
    • Gribskov, M.1    Robinson, N.L.2
  • 12
    • 0034644783 scopus 로고    scopus 로고
    • Analysis and prediction of functional sub-types from protein sequence alignments
    • Hannenhalli, S.S. and Russell, R.B. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol. 303: 61-76.
    • (2000) J. Mol. Biol. , vol.303 , pp. 61-76
    • Hannenhalli, S.S.1    Russell, R.B.2
  • 13
    • 0033597176 scopus 로고    scopus 로고
    • The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
    • Hegyi, H. and Gerstein, M. 1999. The relationship between protein structure and function: A comprehensive survey with application to the yeast genome. J. Mol. Biol. 288: 147-164.
    • (1999) J. Mol. Biol. , vol.288 , pp. 147-164
    • Hegyi, H.1    Gerstein, M.2
  • 14
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8: 275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 15
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones, S. and Thomton, 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    Thomton, J.M.2
  • 16
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 0035853280 scopus 로고    scopus 로고
    • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
    • Landgraf, R., Xenarios, I., and Eisenberg, D. 2001. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 307: 1487-1502.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1487-1502
    • Landgraf, R.1    Xenarios, I.2    Eisenberg, D.3
  • 18
    • 0037447059 scopus 로고    scopus 로고
    • Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases
    • Li, L., Shakhnovich, E.I., and Mirny, L.A. 2003. Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc. Natl. Acad. Sci. 100: 4463-4468.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 4463-4468
    • Li, L.1    Shakhnovich, E.I.2    Mirny, L.A.3
  • 19
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge, O. and Sowa, M.E. 2002. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12: 21-27.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 20
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge, O., Boume, 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    Boume, H.R.2    Cohen, F.E.3
  • 21
    • 0036074510 scopus 로고    scopus 로고
    • Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
    • Luscombe, N.M. and Thornton, J.M. 2002. Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol. 320: 991-1009.
    • (2002) J. Mol. Biol. , vol.320 , pp. 991-1009
    • Luscombe, N.M.1    Thornton, J.M.2
  • 22
    • 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
  • 23
  • 24
    • 0023645203 scopus 로고
    • Interior and surface of monomeric proteins
    • Miller, S., Janin, J., Lesk, A.M., and Chothia, C. 1987. Interior and surface of monomeric proteins. J. Mol. Biol. 196: 641-656.
    • (1987) J. Mol. Biol. , vol.196 , pp. 641-656
    • Miller, S.1    Janin, J.2    Lesk, A.M.3    Chothia, C.4
  • 25
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren, I.M. and Thornton, J.M. 2003. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325: 991-1018.
    • (2003) J. Mol. Biol. , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 26
    • 0036145804 scopus 로고    scopus 로고
    • A comparison of position-specific score matrices based on sequence and structure alignments
    • Panchenko, A.R. and Bryant, S.H. 2002. A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 11: 361-370.
    • (2002) Protein Sci. , vol.11 , pp. 361-370
    • Panchenko, A.R.1    Bryant, S.H.2
  • 27
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4. 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 29
    • 0031604140 scopus 로고    scopus 로고
    • Phylogenetic inference in protein superfamilies: Analysis of SH2 domains
    • Sjolander, K. 1998. Phylogenetic inference in protein superfamilies: Analysis of SH2 domains. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6: 165-174.
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.6 , pp. 165-174
    • Sjolander, K.1
  • 30
    • 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
  • 31
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd, A.E., Orengo, C.A., and Thomton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thomton, J.M.3
  • 32
    • 0036683309 scopus 로고    scopus 로고
    • Plasticity of enzyme active sites
    • -. 2002. Plasticity of enzyme active sites. Trends Biochem. Sci. 27: 419-426.
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 419-426
  • 33
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
    • Tsai, C.J., Lin, S.L., Wolfson, H.J., and Nussinov, R. 1997. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci. 6: 53-64.
    • (1997) Protein Sci. , vol.6 , pp. 53-64
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 34
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.