ClusPro: An automated docking and discrimination method for the prediction of protein complexes

Bioinformatics

Volumn 20, Issue 1, 2004, Pages 45-50

  Comeau, Stephen R ^a   Gatchell, David W ^b   Vajda, Sandor ^a,b   Camacho, Carlos J ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; AUTOMATION; BINDING SITE; COMPUTER SYSTEM; CONTROLLED STUDY; ELECTRICITY; INFORMATION PROCESSING; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; SOLVATION; STRUCTURE ANALYSIS;

ALGORITHMS; BINDING SITES; CLUSTER ANALYSIS; DISCRIMINANT ANALYSIS; ENERGY TRANSFER; MODELS, CHEMICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 0345832301     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg371     Document Type: Article

References (28)

1. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Brooks,B.R., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4, 187-217.
3. Camacho,C.J. and Gatchell,D. (2003) Successful discrimination of protein interactions. Proteins, 52, 92-97.
4. Camacho,C.J., Gatchell,D.W., Kimura,S.R. and Vajda,S. (2000a) Scoring docked conformations generated by rigid-body protein-protein docking. Proteins, 40, 525-537.
5. Camacho,C.J., Kimura,S.R., DeLisi,C. and Vajda,S. (2000b) Kinetics of desolvation-mediated protein-protein binding. Biophys. J., 78, 1094-1105.
6. Camacho,C.J. and Vajda,S. (2001) Protein docking along smooth association pathways. Proc. Natl Acad. Sci. USA, 98, 10636-10641.
7. Camacho,C.J. and Vajda,S. (2002) Protein-protein association kinetics and protein docking. Curr. Opin. Struc. Biol., 12, 36-40.
8. Camacho,C.J., Weng,Z.P., Vajda,S. and DeLisi,C. (1999) Free energy landscapes of encounter complexes in protein-protein association. Biophys. J., 76, 1166-1178.
9. Chakravarti,P. and Janin,J. (2002) Disecting protein-protein recognition sites. Proteins, 47, 334-343.
10. Chen,R., Li,L. and Weng,Z. (2003) ZDOCK: an initial-stage protein docking algorithm. Proteins, 52, 82-87.
11. Chen,R. and Weng,Z. (2003) A novel shape complementarity scoring function for protein-protein docking. Proteins, 51, 397-408.
12. 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.
13. 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.
14. 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.
15. Janin,J., Henrick,K., Moult,J., Ten Eyck,L., Sternberg,M.J., Vajda,S., Vakser,I. and Wodak,S.J. (2003) CAPRI: a Critical Assessment of PRedicted Interactions. Proteins, 52, 2-9.
16. 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.
17. 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.
18. Mandell,J.G., Roberts,V.A., Pique,M.E., Kotlovyi,V., Mitchell,J.C., Nelson,E., Tsigelny,I. and Ten Eyck,L.F. (2001) Protein docking using continuum electrostatics and geometric fit. Protein Eng., 14, 105-113.
19. 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.
20. 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.
21. 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.
22. Ritchie,D.W. and Kemp,G.J.L. (2000) Protein docking using spherical polar Fourier correlations. Proteins, 39, 178-194.
23. 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.
24. Smith,G.R. and Sternberg,M.J.E. (2002) Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol., 12, 28-35.
25. TenEyck,L.F., Mandell,J., Roberts,V.A. and Pique,M.E. (1995) Surveying molecular interactions with DOT. In Hayes,A. and Simmons,M. (eds), Proceedings of the 1995 ACM/IEEE Super-computing Conference. ACM Press, New York.
26. Vakser,I.A. (1996) Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers, 39, 455-464.
27. Weng,Z., Vajda,S. and DeLisi,C. (1996) Prediction of protein complexes using empirical free energy functions. Protein Sci., 5, 614-626.
28. 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.