ZRANK: Reranking protein docking predictions with an optimized energy function

Proteins: Structure, Function and Genetics

Volumn 67, Issue 4, 2007, Pages 1078-1086

  Pierce, Brian ^a   Weng, Zhiping ^a  

^a Boston University   (United States)

Author keywords

Protein docking; Refinement; Reranking; Rigid body docking

Indexed keywords

DOCKING PROTEIN;

ALGORITHM; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; ELECTRICITY; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUALITY CONTROL; SCORING SYSTEM;

COMPUTER SIMULATION; ELECTROSTATICS; PROTEIN BINDING; PROTEINS; SOFTWARE DESIGN;

EID: 34248513078     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21373     Document Type: Article

References (31)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
2. Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
3. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
4. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
5. Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
6. Vakser IA. Protein docking for low-resolution structures. Protein Eng 1995;8:371-377.
7. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
8. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
9. Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
10. Abagyan R, Totrov M, Kuznetsov D. ICM - a new method for protein modeling and design - applications to docking and structure prediction from the distorted native conformation. J Comput Chem 1994;15:488-506.
11. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
12. Fischer D, Lin SL, Wolfson HL, Nussinov R. A geometry-based suite of molecular docking processes. J Mol Biol 1995;248:459-477.
13. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
14. Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF. Protein docking using continuum electrostatics and geometric fit. Protein Eng 2001;14:105-113.
15. Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998;276:265-285.
16. Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins 2003;52:68-73.
17. Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins 2005;60:207-213.
18. Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
19. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4:187-217.
20. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-protein docking benchmark 2.0: an update. Proteins 2005;60:214-216.
21. Neria E, Fischer S, Karplus M. Simulation of activation free energies in molecular systems. J Chem Phys 1996;105:1902-1921.
22. Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
23. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
24. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003;52:88-91.
25. Press WH. Numerical recipes in C: the art of scientific computing. New York: Cambridge University Press; 2002.xxvi,994 p.
26. Doerr TP, Yu Y-K. Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E: Stat Nonlinear Soft Matter Phys 2006;73:061902-061914.
27. Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 2004; 101:11287-11292.
28. Smith GR, Sternberg MJ, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 2005;347:1077-1101.
29. Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Inform 2004;15:160-169.
30. Fanelli F, Ferrari S. Prediction of MEF2A-DNA interface by rigid body docking: a tool for fast estimation of protein mutational effects on DNA binding. J Struct Biol 2006;153:278-283.
31. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.