Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

Proteins: Structure, Function and Genetics

Volumn 72, Issue 3, 2008, Pages 993-1004

  Kozakov, Dima ^a   Schueler Furman, Ora ^b   Vajda, Sandor ^a,c  

^a Boston University   (United States)

^b HEBREW UNIVERSITY   (Israel)

^c Structural Bioinformatics Laboratory   (United States)

Author keywords

Fast Fourier transform; Monte Carlo minimization; Selection of near native structures; Structure refinement

Indexed keywords

ENZYME INHIBITOR;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; FOURIER TRANSFORMATION; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STABILITY; PROTEIN STRUCTURE;

ANTIGEN-ANTIBODY COMPLEX; ENZYME INHIBITORS; ENZYMES; MONTE CARLO METHOD; PROTEINS; THERMODYNAMICS;

EID: 47349119911     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21997     Document Type: Article

References (28)

1. 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.
2. Smith G, Sternberg M. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
3. Camacho C, Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol 2002;12:36-40.
4. Vajda S, Camacho C. Protein-protein docking: is the glass half full or half empty? Trends Biotech 2004;22:110-116.
5. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem A, Aflalo C, Vakser I. Molecular surface recognition - determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
6. Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: An FFT-based protein docking program with pairwise potentials. Proteins 2006;65:392-406.
7. Mendez R, Leplae R, De Maria L, Wodak S. Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins 2003;52:51-67.
8. Mendez R, Leplae R, Lensink M, Wodak S. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
9. Gabb H, Jackson R, Sternberg M. Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 1997;272:106-120.
10. Mandell J, Roberts V, Pique M, Kotlovyi V, Mitchell J, Nelson E, Tsigelny I, Ten Eyck L. Protein docking using continuum electrostatics and geometric fit. Protein Eng 2001;14:105-113.
11. Chen R, Li L, Weng Z. ZDOCK: An initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
12. Li L, Cheng R, Weng Z. RDOCK: Refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
13. Comeau S, Gatchell D, Vajda S, Camacho C. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
14. Kozakov D, Clodfelter K, Vajda S, Camacho C. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
15. Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J 1999; 76:1166-1178.
16. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003;52:88-91.
17. Apaydin MS, Guestrin C, Varma C, Brutlag DL, Latombe J-C. Stochastic roadmap simulation for the study of ligand-protein interactions. Bioinformatics 2002;18:S18-S26.
18. Apaydin MS, Brutlag DL, Guestrin C, Hsu D, Latombe J-C, Varma C. Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. J Comput Biol 2003;10: 257-281.
19. 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.
20. Fernandez-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
21. Zhang C, Vasmatzis G, Cornette J, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
22. Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
23. Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383-10388.
24. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
25. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
26. Rohl CA, Strauss CEM, Misura KMS, Baker D. Protein structure prediction using Rosetta. Methods Enzymol 2004;383:66-93.
27. Ruvinsky A, Kozintsev A. Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions. Proteins 2006;62:202-208.
28. Lorenzen S, Zhang Y. Identification of near-native structures by clustering protein docking conformations. Proteins 2007;68:187-194.