DARS (Decoys As the Reference State) potentials for protein-protein docking

Biophysical Journal

Volumn 95, Issue 9, 2008, Pages 4217-4227

  Chuang, Gwo Yu ^a   Kozakov, Dima ^a   Brenke, Ryan ^b   Comeau, Stephen R ^b   Vajda, Sandor ^a,b  

^a Boston University   (United States)

^b BOSTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; ENZYME INHIBITOR;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; CHEMICAL STRUCTURE; METABOLISM; PROTEIN BINDING;

ANTIGEN-ANTIBODY COMPLEX; ENZYME INHIBITORS; ENZYMES; MODELS, MOLECULAR; PROTEIN BINDING;

EID: 58149152509     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.135814     Document Type: Article

References (37)

1. Sippl, M. J. 1990. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213:859-883.
2. Skolnick, J., L. Jaroszewski, A. Kolinski, and A. Godzik. 1997. Derivation and testing of pair potentials for protein folding, when is the quasichemical approximation correct? Protein Sci. 6:1-13.
3. Lu, H., and J. Skolnick. 2001. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 44:223-232.
4. Godzik, A. 1996. Knowledge-based potentials for protein folding: what can we learn from known protein structures? Structure. 4:363-366.
5. Miyazawa, S., and R. Jernigan. 1985. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:534-552.
6. Miyazawa, S., and R. Jernigan. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:623-644.
7. Rojnuckarin, A., and S. Subramaniam. 1999. Knowledge-based interaction potentials for proteins. Proteins. 36:54-67.
8. Zhou, H., and Y. Zhou. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11:2714-2726.
9. Camacho, C., D. Gatchell, S. Kimura, and S. Vajda. 2000. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins. 40:525-537.
10. Li, L., R. Cheng, and Z. Weng. 2003. RDOCK: refinement of rigid-body protein docking predictions. Proteins. 53:693-707.
11. Comeau, S., D. Gatchell, S. Vajda, and C. Camacho. 2004. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 20:45-50.
12. Moont, G., H. Gabb, and M. Sternberg. 1999. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins. 35:364-373.
13. Murphy, J., D. Gatchell, J. Prasad, and S. Vajda. 2003. Combination of scoring functions improves discrimination in protein-protein docking. Proteins. 53:840-854.
14. Lu, H., L. Lu, and J. Skolnick. 2003. Development of unified statistical potentials describing protein-protein interactions. Biophys. J. 84:1895-1901.
15. Liu, S., C. Zhang, H. Zhou, and Y. Zhou. 2004. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins. 56:93-101.
16. Kozakov, D., R. Brenke, S. R. Comeau, and S. Vajda. 2006. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins. 65:392-406.
17. Mintseris, J., B. Pierce, K. Wiehe, R. Anderson, R. Chen, and Z. Weng. 2007. Integrating statistical pair potentials into protein complex prediction. Proteins. 69:511-520.
18. Smith, R., R. Hubbard, D. Gschwend, A. Leach, and A. Good. 2003. Analysis and optimization of structure-based virtual screening protocols. 3. New methods and old problems in scoring function design. J. Mol. Graph. Model. 22:41-53.
19. Pham, T., and A. Jain. 2008. Customizing scoring functions for docking. J. Comput. Aided Mol. Des. 22:269-286.
20. Pham, T., and A. Jain. 2006. Parameter estimation for scoring protein-ligand interactions using negative training data. J. Med. Chem. 49:5856-5868.
21. Vajda, S., and C. Camacho. 2004. Protein-protein docking: is the glass half full or half empty? Trends Biotechnol. 22:110-116.
22. Kozakov, D., K. Clodfelter, S. Vajda, and C. Camacho. 2005. Optimal clustering for detecting near-native conformations in protein docking. Biophys. J. 89:867-875.
23. Chen, R., J. Mintseris, J. Janin, and Z. Weng. 2003. A protein-protein docking benchmark. Proteins. 52:88-91.
24. Zhang, C., G. Vasmatzis, J. Cornette, and C. DeLisi. 1997. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267:707-726.
25. Mintseris, J., and Z. Weng. 2004. Optimizing protein representations with information theory. Genome Inform. 15:160-169.
26. Ruvinsky, A. M., and A. V. Kozintsev. 2005. The key role of atom types, reference states, and interaction cutoff radii in the knowledge-based method: New variational approach. Proteins. 58:845-851.
27. Glaser, F., D. M. Steinberg, I. A. Vakser, and N. Ben-Tal. 2001. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins. 43:89-102.
28. Janin, J., K. Henrick, J. Moult, L. Ten Eyck, M. Sternberg, S. Vajda, I. Vakser, and S. Wodak. 2003. CAPRI: a critical assessment of predicted interactions. Proteins. 52:2-9.
29. Camacho, C., and S. Vajda. 2002. Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. USA. 23:319-334.
30. Paschalidis, I. C., Y. Shen, P. Vakili, and S. Vajda. 2007. SDU: a semi-definite programming-based underestimation method for global optimization in molecular docking. IEEE Trans. Automat. Contr. 52:664-676.
31. Jain, A., and A. Nicholls. 2008. Recommendations for evaluation of computational methods. J. Comput. Aided Mol. Des. 22:133-139.
32. Bradley, J. 1968. Distribution Free Statistical Tests. Prentice Hall, Englewood Cliffs, NJ.
33. Jackson, R. 1999. Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem. Protein Sci. 8:603-613.
34. LoConte, L., C. Chothia, and J. Janin. 1999. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:2177-2198.
35. O'Toole, N., and I. A. Vakser. 2008. Large-scale characteristics of the energy landscape in protein-protein interactions. Proteins. 71:144-152.
36. Ponomarenko, J. V., and P. E. Bourne. 2007. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct. Biol. 7:64.
37. Camacho, C., and C. Zhang. 2005. FastContact: rapid estimate of contact and binding free energies. Bioinformatics. 21:2534-2536.