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Volumn 21, Issue SUPPL. 1, 2005, Pages

In silico identification of functional regions in proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA; INDOLE 3 GLYCEROL PHOSPHATE SYNTHASE; LIGAND; PROTEIN SH2;

EID: 29144462537     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1023     Document Type: Article
Times cited : (51)

References (44)
  • 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
    • 0030598920 scopus 로고    scopus 로고
    • Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii
    • Berg,A., Vervoort,J. and de Kok,A. (1996) Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. J. Mol. Biol., 261, 432-442.
    • (1996) J. Mol. Biol. , vol.261 , pp. 432-442
    • Berg, A.1    Vervoort, J.2    de Kok, A.3
  • 5
    • 0029896163 scopus 로고    scopus 로고
    • Regulation, substrates and functions of src
    • Brown,M.T. and Cooper,J.A. (1996) Regulation, substrates and functions of src. Biochim. Biophys. Acta, 1287, 121-149.
    • (1996) Biochim. Biophys. Acta , vol.1287 , pp. 121-149
    • Brown, M.T.1    Cooper, J.A.2
  • 6
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • Chakrabarti, P. and Janin, J. (2002) Dissecting protein-protein recognition sites. Proteins, 47, 334-343.
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 7
    • 0031863441 scopus 로고    scopus 로고
    • Mutational analysis of the active site of indoleglycerol phosphate synthase from Escherichia coli
    • Darimont,B., Stehlin,C., Szadkowski,H. and Kirschner,K. (1998) Mutational analysis of the active site of indoleglycerol phosphate synthase from Escherichia coli. Protein Sci., 7, 1221-1232.
    • (1998) Protein Sci. , vol.7 , pp. 1221-1232
    • Darimont, B.1    Stehlin, C.2    Szadkowski, H.3    Kirschner, K.4
  • 9
    • 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
  • 10
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • DeLano,W.L. (2002) Unraveling hot spots in binding interfaces: Progress and challenges. Curr. Opin. Struct. Biol., 12, 14-20.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 14-20
    • DeLano, W.L.1
  • 11
    • 0036145469 scopus 로고    scopus 로고
    • Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function
    • Friedberg,I. and Margalit,H. (2002) Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function. Protein Sci., 11, 350-360.
    • (2002) Protein Sci. , vol.11 , pp. 350-360
    • Friedberg, I.1    Margalit, H.2
  • 12
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser,F., Pupko,T., Paz,I., Bell,R.E., Bechor-Shental,D., Martz,E. and Ben-Tal,N. (2003) ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 13
    • 0008524099 scopus 로고
    • Crystallographic refinement by incorporation of molecular dynamics: Thermostable serine protease thermitase complexed with eglin c
    • Gros,P., Fujinaga,M., Dijkstra,B.W., Kalk,K.H. and Hol,W.G. (1989) Crystallographic refinement by incorporation of molecular dynamics: thermostable serine protease thermitase complexed with eglin c. Acta. Crystallogr. B, 45, 488-499.
    • (1989) Acta. Crystallogr. B , vol.45 , pp. 488-499
    • Gros, P.1    Fujinaga, M.2    Dijkstra, B.W.3    Kalk, K.H.4    Hol, W.G.5
  • 14
    • 0036308014 scopus 로고    scopus 로고
    • The catalytic mechanism of indole-3-glycerol phosphate synthase: Crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product
    • Hennig,M., Darimont,B.D., Jansonius,J.N. and Kirschner,K. (2002) The catalytic mechanism of indole-3-glycerol phosphate synthase: Crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product. J. Mol. Biol., 319, 757-766.
    • (2002) J. Mol. Biol. , vol.319 , pp. 757-766
    • Hennig, M.1    Darimont, B.D.2    Jansonius, J.N.3    Kirschner, K.4
  • 15
    • 1642325994 scopus 로고    scopus 로고
    • Prediction of functional sites in proteins using conserved functional group analysis
    • Innis,C.A., Anand,A.P. and Sowdhamini,R. (2004) Prediction of functional sites in proteins using conserved functional group analysis. J. Mol. Biol., 337, 1053-1068.
    • (2004) J. Mol. Biol. , vol.337 , pp. 1053-1068
    • Innis, C.A.1    Anand, A.P.2    Sowdhamini, R.3
  • 16
    • 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
  • 17
    • 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
  • 18
    • 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
  • 19
    • 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
  • 20
    • 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
  • 21
    • 0037609791 scopus 로고    scopus 로고
    • Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
    • Ma,B., Elkayam,T., Wolfson,H. and Nussinov,R. (2003) Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl Acad. Sci. USA, 100, 5772-5777.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.3    Nussinov, R.4
  • 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
    • 1242339659 scopus 로고    scopus 로고
    • A family of evolution-entropy hybrid methods for ranking protein residues by importance
    • Mihalek,I., Res,I. and Lichtarge,O. (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J. Mol. Biol., 336, 1265-1282.
    • (2004) J. Mol. Biol. , vol.336 , pp. 1265-1282
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 24
    • 0037485769 scopus 로고    scopus 로고
    • Combining inference from evolution and geometric probability in protein structure evaluation
    • Mihalek,I., Res,I., Yao,H. and Lichtarge,O. (2003) Combining inference from evolution and geometric probability in protein structure evaluation. J. Mol. Biol., 331, 263-279.
    • (2003) J. Mol. Biol. , vol.331 , pp. 263-279
    • Mihalek, I.1    Res, I.2    Yao, H.3    Lichtarge, O.4
  • 25
  • 26
    • 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
  • 27
    • 0041418225 scopus 로고    scopus 로고
    • Identification of functionally conserved residues with the use of entropy-variability plots
    • Oliveira,L., Paiva,P.B., Paiva,A.C. and Vriend,G. (2003) Identification of functionally conserved residues with the use of entropy-variability plots. Proteins, 52, 544-552.
    • (2003) Proteins , vol.52 , pp. 544-552
    • Oliveira, L.1    Paiva, P.B.2    Paiva, A.C.3    Vriend, G.4
  • 28
    • 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
  • 29
    • 6944227836 scopus 로고    scopus 로고
    • Automated prediction of protein function and detection of functional sites from structure
    • Pazos,F. and Sternberg,M.J. (2004) Automated prediction of protein function and detection of functional sites from structure. Proc. Natl Acad. Sci. USA, 101, 14754-14759.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 14754-14759
    • Pazos, F.1    Sternberg, M.J.2
  • 30
    • 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 (suppl), S71-S77.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL.
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 31
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost,B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol., 318, 595-608.
    • (2002) J. Mol. Biol. , vol.318 , pp. 595-608
    • Rost, B.1
  • 32
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander,C. and Schneider,R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 34
    • 0038675537 scopus 로고    scopus 로고
    • Conserved residue clustering and protein structure prediction
    • Schueler-Furman,O. and Baker,D. (2003) Conserved residue clustering and protein structure prediction. Proteins, 52, 225-235.
    • (2003) Proteins , vol.52 , pp. 225-235
    • Schueler-Furman, O.1    Baker, D.2
  • 35
    • 4444343959 scopus 로고    scopus 로고
    • Identifying DNA-binding proteins using structural motifs and the electrostatic potential
    • Shanahan,H.P., Garcia,M.A., Jones,S. and Thornton,J.M. (2004) Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res., 32, 4732-4741.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4732-4741
    • Shanahan, H.P.1    Garcia, M.A.2    Jones, S.3    Thornton, J.M.4
  • 36
    • 0000328844 scopus 로고
    • A new vertex algorithm to calculate solvent accessible surface area
    • Sridharan,S., Nicholls,A. and Honig,B. (1992) A new vertex algorithm to calculate solvent accessible surface area. Biophys. J., 61, A174.
    • (1992) Biophys. J. , vol.61
    • Sridharan, S.1    Nicholls, A.2    Honig, B.3
  • 38
    • 0037197254 scopus 로고    scopus 로고
    • Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
    • Tsodikov,O.V., Record,M.T., Jr and Sergeev,Y.V. (2002) Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Compt. Chem., 23, 600-609.
    • (2002) J. Compt. Chem. , vol.23 , pp. 600-609
    • Tsodikov, O.V.1    Record Jr., M.T.2    Sergeev, Y.V.3
  • 39
    • 0035914476 scopus 로고    scopus 로고
    • Conservation helps to identify biologically relevant crystal contacts
    • Valdar,W.S. and Thornton,J.M. (2001a) Conservation helps to identify biologically relevant crystal contacts. J. Mol. Biol., 313, 399-416.
    • (2001) J. Mol. Biol. , vol.313 , pp. 399-416
    • Valdar, W.S.1    Thornton, J.M.2
  • 40
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers
    • Valdar,W.S. and Thornton,J.M. (2001b) Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins, 42, 108-124.
    • (2001) Proteins , vol.42 , pp. 108-124
    • Valdar, W.S.1    Thornton, J.M.2
  • 41
    • 0027409064 scopus 로고
    • Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: Crystal structures of the complexed and peptide-free forms
    • Waksman,G., Shoelson,S.E., Pant,N., Cowburn,D. and Kuriyan,J. (1993) Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: crystal structures of the complexed and peptide-free forms. Cell, 72, 779-790.
    • (1993) Cell , vol.72 , pp. 779-790
    • Waksman, G.1    Shoelson, S.E.2    Pant, N.3    Cowburn, D.4    Kuriyan, J.5
  • 42
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace,A.C., Laskowski,R.A. and Thornton,J.M. (1995)LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134.
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 43
    • 0031025991 scopus 로고    scopus 로고
    • Three-dimensional structure of the tyrosine kinase c-Src
    • Xu,W., Harrison,S.C. and Eck,M.J. (1997) Three-dimensional structure of the tyrosine kinase c-Src. Nature, 385, 595-602.
    • (1997) Nature , vol.385 , pp. 595-602
    • Xu, W.1    Harrison, S.C.2    Eck, M.J.3


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