Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI

Proteins: Structure, Function and Genetics

Volumn 69, Issue 4, 2007, Pages 734-742

  Shen, Yang ^a,b   Brenke, Ryan ^a,b   Kozakov, Dima ^a   Comeau, Stephen R ^c   Beglov, Dmitri ^a   Vajda, Sandor ^a  

^a Boston University   (United States)

^b BOSTON UNIVERSITY   (United States)

^c Dyax Corp   (United States)

Author keywords

Clustering; DARS pairwise potential; Energy funnel; Fast Fourier transform; Global optimization; Protein docking by PIPER; Refinement by SDU; Semidefinite programming

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; BACTERIAL PROTEIN; DOCKING PROTEIN; GUANOSINE TRIPHOSPHATASE ACTIVATING PROTEIN; HEMK ENZYME; LIGASE; MEMBRANE PROTEIN; METHYLTRANSFERASE; ORIGIN RECOGNITION COMPLEX; PROTEIN ARHGAP10; PROTEIN HIP2; PROTEIN ORC1; PROTEIN PAL; PROTEIN RF1; PROTEIN TOLB; PROTEIN UBC9; RELEASING FACTOR; SILENT INFORMATION REGULATOR PROTEIN; UNCLASSIFIED DRUG;

CLUSTER ANALYSIS; COMPLEX FORMATION; CONFERENCE PAPER; FOURIER TRANSFORMATION; METHODOLOGY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; SEQUENCE HOMOLOGY;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; ESCHERICHIA COLI; FOURIER ANALYSIS; MODELS, STATISTICAL; MONTE CARLO METHOD; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 36749050815     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21754     Document Type: Conference Paper

References (36)

1. Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40(3):525-537.
2. Murphy J, Gatchell D, Prasad J, Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins 2003;53:840-854.
3. Camacho C, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001;98:10636-10641.
4. 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.
5. Kozakov D, Clodfelter K, Vajda S, Camacho C. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
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. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003;52:88-91.
8. Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
9. Li L, Cheng R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
10. Moont G, Gabb H, Sternberg M. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
11. Lu H, Lu L, Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys J 2003;84:1895-1901.
12. Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 2004;56:93-101.
13. Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins, to be published.
14. Paschalidis IC, Shen Y, Vakili P, Vajda S. A semi-definite programming-based underestimation method for stochastic global optimization in protein docking. IEEE Trans Automatic Control 2007;52:664-676.
15. Paschalidis IC, Shen Y, Vakili P, Vajda S. Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. In Proceedings of the 28th IEEE Engineering in Medicine and Biology Society (EMBS) Conference, New York City, New York, 2006, pp 5330-5333.
16. Lindemann S, Yershova A, LaValle S. Incremental grid sampling strategies in robotics. In Proceedings of the Sixth International Workshop on the Algorithmic Foundations of Robotics, July 11-13, 2004; Utrecht/Zeist, Netherlands.
17. Zhang C, Vasmatzis G, Cornette J. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
18. Vajda S, Camacho C. Protein-protein docking: is the glass half full or half empty? Trends Biotechnol 2004;22:110-116.
19. Vajda S. Classification of protein complexes based on docking difficulty. Proteins 2005;60:176-180.
20. LoConte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
21. Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
22. 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.
23. Miyazawa S, Jernigan R. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
24. Vestergaard B, Van L, Andersen G, Nyborg J, Buckingham R, Kjeldgaard M. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol Cell 2001;8:1375-1382.
25. Sanchez R, Sali A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins 1997;1:50-58.
26. Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham R. Molecular basis for bacterial class I release factor methylation by PrmC. Mol Cell 2005;20:917-927.
27. Gray J, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl C, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
28. Hou Z, Bernstein D, Fox C, Keck J. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 2005;102:8489-8494.
29. Menetrey J, Perderiset M, Cicolari J, Dubois T, Elkhatib N, El Khadali F, Franco M, Chavrier P, Houdusse A. Structural basis for ARF1-mediated recruitment of ARHGAP21 to golgi membranes. EMBO J 2007;26:1953-1962.
30. Bonsor D, Grishkovskaya I, Dodson E, Kleanthous C. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
31. Ray M, Germon P, Vianney A, Portalier R, Lazzaroni J. Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction. J Bacteriol 2000;182:821-824.
32. Walker J, Awakumov G, Xue S, Newman E, Mackenzie F, Weigelt J, Sundstrom M, Arrowsmith C. Novel and unexpected complex between the sumo-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa, to be published.
33. Pichler A, Knipscheer P, Oberhofer E, van Dijk W, Korner R, Olsen J, Jentsch S, Melchior F, Signma T. SUMO modifications of the ubiquitin-conjugating enzyme E2-25K. Nat Struct Mol Biol 2005;12:264-269.
34. 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.
35. 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.
36. Camacho C, Gatchell D, Kimura S, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000;40:525-537.