메뉴 건너뛰기




Volumn 32, Issue WEB SERVER ISS., 2004, Pages

ClusPro: A fully automated algorithm for protein-protein docking

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CHEMICAL INTERACTION; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; E-MAIL; ELECTRICITY; ENERGY; INTERNET; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 3242877815     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh354     Document Type: Article
Times cited : (691)

References (30)
  • 1
    • 0036468396 scopus 로고    scopus 로고
    • Protein-protein association kinetics and protein docking
    • Camacho,C.J. and Vajda,S. (2002) Protein-protein association kinetics and protein docking. Curr. Opin. Struct. Biol., 12, 36-40.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 36-40
    • Camacho, C.J.1    Vajda, S.2
  • 2
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin,I., Ma,B., Wolfson,H. and Nussinov,R. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 3
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith,G.R. and Sternberg,M.J.E. (2002) Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol., 12, 28-35.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 4
    • 0026572775 scopus 로고
    • Molecular surface recognition - Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir,E., Shariv,I., Eisenstein,M., Friesem,A., Aflalo,C. and Vakser,I.A. (1992) Molecular surface recognition - determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl Acad. Sci. USA, 89, 2195-2199.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.4    Aflalo, C.5    Vakser, I.A.6
  • 5
    • 0030248996 scopus 로고    scopus 로고
    • Low-resolution docking: Prediction of complexes for underdetermined structures
    • Vakser,I.A. (1996) Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers, 39, 455-464.
    • (1996) Biopolymers , vol.39 , pp. 455-464
    • Vakser, I.A.1
  • 6
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie,D.W. and Kemp,G.J.L. (2000) Protein docking using spherical polar Fourier correlations. Proteins, 39, 178-194.
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.L.2
  • 7
    • 0029933286 scopus 로고    scopus 로고
    • Prediction of protein complexes using empirical free energy functions
    • Weng,Z., Vajda,S. and DeLisi,C. (1996) Prediction of protein complexes using empirical free energy functions. Protein Sci., 5, 614-626.
    • (1996) Protein Sci. , vol.5 , pp. 614-626
    • Weng, Z.1    Vajda, S.2    DeLisi, C.3
  • 8
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics, and biochemical information
    • Gabb,H.A., Jackson,R.M. and Sternberg,M.J.E. (1997) Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J. Mol. Biol., 272, 106-120.
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 9
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • Jackson,R.M., Gabb,H.A. and Sternberg,M.J.E. (1998) Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem. J. Mol. Biol., 276, 265-285.
    • (1998) J. Mol. Biol. , vol.276 , pp. 265-285
    • Jackson, R.M.1    Gabb, H.A.2    Sternberg, M.J.E.3
  • 10
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • Moont,G., Gabb,H.A. and Sternberg,M.J.E. (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins, 35, 364-373.
    • (1999) Proteins , vol.35 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.E.3
  • 11
    • 0034663658 scopus 로고    scopus 로고
    • Scoring docked conformations generated by rigid-body protein-protein docking
    • Camacho,C.J., Gatchell,D.W., Kimura,S.R. and Vajda,S. (2000) Scoring docked conformations generated by rigid-body protein-protein docking. Proteins, 40, 525-537.
    • (2000) Proteins , vol.40 , pp. 525-537
    • Camacho, C.J.1    Gatchell, D.W.2    Kimura, S.R.3    Vajda, S.4
  • 12
    • 0034769223 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
    • Norel,R., Sheinerman,F., Petrey,D. and Honig,B. (2001) Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis. Protein Sci., 10, 47-61.
    • (2001) Protein Sci. , vol.10 , pp. 47-61
    • Norel, R.1    Sheinerman, F.2    Petrey, D.3    Honig, B.4
  • 13
    • 0035141353 scopus 로고    scopus 로고
    • Dynamical view of the positions of key side chains in protein-protein recognition
    • Kimura,S.R., Brower,R.C., Vajda,S. and Camacho,C.J. (2001) Dynamical view of the positions of key side chains in protein-protein recognition. Biophys. J., 80, 635-642.
    • (2001) Biophys. J. , vol.80 , pp. 635-642
    • Kimura, S.R.1    Brower, R.C.2    Vajda, S.3    Camacho, C.J.4
  • 14
    • 0032981961 scopus 로고    scopus 로고
    • Free energy landscapes of encounter complexes in protein-protein association
    • Camacho,C.J., Weng,ZP, Vajda,S. and DeLisi,C. (1999) Free energy landscapes of encounter complexes in protein-protein association. Biophys. J., 76, 1166-1178.
    • (1999) Biophys. J. , vol.76 , pp. 1166-1178
    • Camacho, C.J.1    Weng, Z.P.2    Vajda, S.3    DeLisi, C.4
  • 15
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • Shortle,D., Simons,K.T. and Baker,D. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl Acad. Sci., USA, 95, 11158-11162.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 17
    • 0038359596 scopus 로고    scopus 로고
    • Successful discrimination of protein interactions
    • Camacho,C.J. and Gatchell,D. (2003) Successful discrimination of protein interactions. Proteins, 52, 92-97.
    • (2003) Proteins , vol.52 , pp. 92-97
    • Camacho, C.J.1    Gatchell, D.2
  • 18
    • 0345832301 scopus 로고    scopus 로고
    • ClusPro: An automated docking and discrimination method for the prediction of protein complexes
    • Comeau,S.R., Gatchell,D.W., Vajda,S. and Camacho,C.J. (2004) ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20, 45-50.
    • (2004) Bioinformatics , vol.20 , pp. 45-50
    • Comeau, S.R.1    Gatchell, D.W.2    Vajda, S.3    Camacho, C.J.4
  • 19
    • 0029430865 scopus 로고
    • Surveying molecular interactions with DOT
    • Hayes,A. and Simmons,M. ed., Proceedings of the 1995 ACM/IEEE Supercomputing Conference. ACM Press, New York
    • Ten Eyck,L.F., Mandell,J., Roberts,V.A. and Pique,M.E. (1995) Surveying molecular interactions with DOT. In Hayes,A. and Simmons,M. (ed.), Proceedings of the 1995 ACM/IEEE Supercomputing Conference. ACM Press, New York.
    • (1995)
    • Ten Eyck, L.F.1    Mandell, J.2    Roberts, V.A.3    Pique, M.E.4
  • 21
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen,R. and Weng,Z. (2003) A novel shape complementarity scoring function for protein-protein docking. Proteins, 51, 397-408.
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 22
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein docking algorithm
    • Chen,R., Li,L. and Weng,Z. (2003) ZDOCK: an initial-stage protein docking algorithm. Proteins, 52, 82-87.
    • (2003) Proteins , vol.52 , pp. 82-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 23
    • 0037093645 scopus 로고    scopus 로고
    • Disecting protein-protein recognition sites
    • Chakravarti,P. and Janin,J. (2002) Disecting protein-protein recognition sites. Proteins, 47, 334-343.
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakravarti, P.1    Janin, J.2
  • 24
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • Zhang,C., Cornette,J.L. and DeLisi,C. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol., 267, 707-726.
    • (1997) J. Mol. Biol. , vol.267 , pp. 707-726
    • Zhang, C.1    Cornette, J.L.2    DeLisi, C.3
  • 25
    • 0034049350 scopus 로고    scopus 로고
    • Kinetics of desolvation-mediated protein-protein binding
    • Camacho,C.J., Kimura,S.R., DeLisi,C. and Vajda,S. (2000) Kinetics of desolvation-mediated protein-protein binding. Biophys. J., 78, 1094-1105.
    • (2000) Biophys. J. , vol.78 , pp. 1094-1105
    • Camacho, C.J.1    Kimura, S.R.2    DeLisi, C.3    Vajda, S.4
  • 28
    • 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
  • 29
    • 0041858013 scopus 로고    scopus 로고
    • Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface
    • Takagi,J., Yang,Y., Liu,J.H., Wang,J.H. and Springer,T.A. (2003) Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface. Nature, 424, 969-974.
    • (2003) Nature , vol.424 , pp. 969-974
    • Takagi, J.1    Yang, Y.2    Liu, J.H.3    Wang, J.H.4    Springer, T.A.5
  • 30
    • 0035845563 scopus 로고    scopus 로고
    • Protein docking along smooth association pathways
    • Camacho,C.J. and Vajda,S. (2001) Protein docking along smooth association pathways. Proc. Natl Acad. Sci., USA, 98, 10636-10641.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10636-10641
    • Camacho, C.J.1    Vajda, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.