메뉴 건너뛰기




Volumn 357, Issue 5, 2006, Pages 1669-1682

Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment

Author keywords

distance restraints; environment specific substitution tables; protein protein docking

Indexed keywords

AMINO ACID; DOCKING PROTEIN;

EID: 33645095436     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.01.001     Document Type: Article
Times cited : (56)

References (27)
  • 1
    • 0036468396 scopus 로고    scopus 로고
    • Protein-protein association kinetics and protein docking
    • C.J. Camacho, and S. Vajda Protein-protein association kinetics and protein docking Curr. Opin. Struct. Biol. 12 2002 36 40
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 36-40
    • Camacho, C.J.1    Vajda, S.2
  • 2
    • 0035281357 scopus 로고    scopus 로고
    • Computer simulation of protein-protein interactions
    • A.H. Elcock, D. Sept, and J.A. McCammon Computer simulation of protein-protein interactions J. Phys. Chem. ser. B 105 2001 1504 1518
    • (2001) J. Phys. Chem. Ser. B , vol.105 , pp. 1504-1518
    • Elcock, A.H.1    Sept, D.2    McCammon, J.A.3
  • 3
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • J. Fernandez-Recio, M. Totrov, and R. Abagyan Soft protein-protein docking in internal coordinates Protein Sci. 11 2002 280 291
    • (2002) Protein Sci. , vol.11 , pp. 280-291
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 4
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • J. Fernandez-Recio, M. Totrov, and R. Abagyan Identification of protein-protein interaction sites from docking energy landscapes J. Mol. Biol. 335 2004 843 865
    • (2004) J. Mol. Biol. , vol.335 , pp. 843-865
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 5
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • G.R. Smith, and M.J. Sternberg Prediction of protein-protein interactions by docking methods Curr. Opin. Struct. Biol. 12 2002 28 35
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 6
    • 0032054715 scopus 로고    scopus 로고
    • Predictive docking of protein-protein and protein-DNA complexes
    • M.J. Sternberg, H.A. Gabb, and R.M. Jackson Predictive docking of protein-protein and protein-DNA complexes Curr. Opin. Struct. Biol. 8 1998 250 256
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 250-256
    • Sternberg, M.J.1    Gabb, H.A.2    Jackson, R.M.3
  • 7
    • 0018165127 scopus 로고
    • Computer analysis of protein-protein interaction
    • S.J. Wodak, and J. Janin Computer analysis of protein-protein interaction J. Mol. Biol. 124 1978 323 342
    • (1978) J. Mol. Biol. , vol.124 , pp. 323-342
    • Wodak, S.J.1    Janin, J.2
  • 8
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • C. Dominguez, R. Boelens, and A.M. Bonvin HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J Am. Chem. Soc. 125 2003 1731 1737
    • (2003) J Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 9
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • L.A. Mirny, and E.I. Shakhnovich Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function J. Mol. Biol. 291 1999 177 196
    • (1999) J. Mol. Biol. , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 10
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • O. Lichtarge, and M.E. Sowa Evolutionary predictions of binding surfaces and interactions Curr. Opin. Struct. Biol. 12 2002 21 27
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 11
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers
    • W.S. Valdar, and J.M. Thornton Protein-protein interfaces: analysis of amino acid conservation in homodimers Proteins: Struct. Funct. Genet. 42 2001 108 124
    • (2001) Proteins: Struct. Funct. Genet. , vol.42 , pp. 108-124
    • Valdar, W.S.1    Thornton, J.M.2
  • 12
    • 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
    • P. Aloy, E. Querol, F.X. Aviles, and M.J. Sternberg 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 2001 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
  • 13
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • D.R. Caffrey, S. Somaroo, J.D. Hughes, J. Mintseris, and E.S. Huang Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci. 13 2004 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
  • 14
    • 0027062943 scopus 로고
    • Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
    • J. Overington, D. Donnelly, M.S. Johnson, A. Sali, and T.L. Blundell Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Sci. 1 1992 216 226
    • (1992) Protein Sci. , vol.1 , pp. 216-226
    • Overington, J.1    Donnelly, D.2    Johnson, M.S.3    Sali, A.4    Blundell, T.L.5
  • 15
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • J. Overington, M.S. Johnson, A. Sali, and T.L. Blundell Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction Proc. Roy. Soc. ser. B 241 1990 132 145
    • (1990) Proc. Roy. Soc. Ser. B , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 16
    • 4544230537 scopus 로고    scopus 로고
    • Distinguishing structural and functional restraints in evolution in order to identify interaction sites
    • V. Chelliah, L. Chen, T.L. Blundell, and S.C. Lovell Distinguishing structural and functional restraints in evolution in order to identify interaction sites J. Mol. Biol. 342 2004 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
  • 19
    • 0034459679 scopus 로고    scopus 로고
    • Evolutionary trace analysis of TGF-beta and related growth factors: Implications for site-directed mutagenesis
    • C.A. Innis, J. Shi, and T.L. Blundell Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis Protein Eng. 13 2000 839 847
    • (2000) Protein Eng. , vol.13 , pp. 839-847
    • Innis, C.A.1    Shi, J.2    Blundell, T.L.3
  • 20
    • 0025998314 scopus 로고
    • Multiple murine alpha 1-protease inhibitor genes show unusual evolutionary divergence
    • F. Borriello, and K.S. Krauter Multiple murine alpha 1-protease inhibitor genes show unusual evolutionary divergence Proc. Natl Acad. Sci. USA 88 1991 9417 9421
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 9417-9421
    • Borriello, F.1    Krauter, K.S.2
  • 21
    • 0023188637 scopus 로고
    • Accelerated evolution in the reactive centre regions of serine protease inhibitors
    • R.E. Hill, and N.D. Hastie Accelerated evolution in the reactive centre regions of serine protease inhibitors Nature 326 1987 96 99
    • (1987) Nature , vol.326 , pp. 96-99
    • Hill, R.E.1    Hastie, N.D.2
  • 22
    • 0026025875 scopus 로고
    • The murine pi-2 proteinase inhibitor locus: A multigene family with a hypervariable reactive site domain
    • J.D. Inglis, and R.E. Hill The murine pi-2 proteinase inhibitor locus: a multigene family with a hypervariable reactive site domain EMBO J. 10 1991 255 261
    • (1991) EMBO J. , vol.10 , pp. 255-261
    • Inglis, J.D.1    Hill, R.E.2
  • 24
    • 0042010066 scopus 로고    scopus 로고
    • Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem
    • J.R. Bradford, and D.R. Westhead Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem Protein Sci. 12 2003 2099 2103
    • (2003) Protein Sci. , vol.12 , pp. 2099-2103
    • Bradford, J.R.1    Westhead, D.R.2
  • 25
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • R. Chen, and Z. Weng A novel shape complementarity scoring function for protein-protein docking Proteins: Struct. Funct. Genet. 51 2003 397 408
    • (2003) Proteins: Struct. Funct. Genet. , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 26
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • H.A. Gabb, R.M. Jackson, and M.J. Sternberg Modelling protein docking using shape complementarity, electrostatics and biochemical information J. Mol. Biol. 272 1997 106 120
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 27
    • 0001962564 scopus 로고    scopus 로고
    • The molecular modeling toolkit: A new approach to molecular simulations
    • K. Hinsen The molecular modeling toolkit: a new approach to molecular simulations J. Comput. Chem. 21 2000 79 85
    • (2000) J. Comput. Chem. , vol.21 , pp. 79-85
    • Hinsen, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.