CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 6, 2013, Pages 1005-1016

  Omori, Satoshi ^a   Kitao, Akio ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Benchmark; Centroid method; Complex interface; K means method; Rigid body docking

Indexed keywords

ARTICLE; CYCLUS METHOD; INTERMETHOD COMPARISON; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

CLUSTER ANALYSIS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 84878141430     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24252     Document Type: Article

References (51)

1. Camacho CJ, Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol 2002; 12: 36-40.
2. Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002; 12: 28-35.
3. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006; 16: 194-200.
4. Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006; 16: 183-193.
5. Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins 2008; 73: 271-289.
6. Moreira IS, Fernandes PA, Ramos MJ. Protein-protein docking dealing with the unknown. J Comput Chem 2009; 31: 317-342.
7. Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009; 19: 164-170.
8. Zacharias M. Accounting for conformational changes during protein-protein docking. Curr Opin Struct Biol 2010; 20: 180-186.
9. Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001; 98: 10636-10641.
10. Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003; 125: 1731-1737.
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. Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003; 12: 1271-1282.
13. Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007; 69: 139-159.
14. Mashiach E, Nussinov R, Wolfson HJ. FiberDock: flexible induced-fit backbone refinement in molecular docking. Proteins 2010; 78: 1503-1519.
15. Moal IH, Bates PA. SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci 2010; 11: 3623-3648.
16. Venkatraman V, Ritchie DW. Flexible protein docking refinement using pose-dependent normal mode analysis. Proteins 2012; 80: 2262-2274.
17. 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.
18. Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997; 272: 106-120.
19. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003; 52: 80-87.
20. Venkatraman V, Yang YD, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics 2009; 10: 407.
21. Duhovny D, Nussinov R, Wolfson HJ. Efficient unbound docking of rigid molecules. Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science Vol. 2452. Rome, Italy: Springer Verlag; 2002. pp 185-200.
22. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 2005; 33: W363-W367.
23. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003; 52: 88-91.
24. 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.
25. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008; 73: 705-709.
26. Hwang H, Vreven T, Janin J, Weng ZP. Protein-protein docking benchmark version 4.0. Proteins 2010; 78: 3111-3114.
27. Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003; 53: 693-707.
28. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for acromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4: 187-217.
29. Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007; 67: 1078-1086.
30. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 2004; 32: W96-W99.
31. 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.
32. Solernou A, Fernandez-Recio J. Protein docking by rotation-based uniform sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. BMC Bioinformatics 2010; 11: 352.
33. Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol 2011; 173: 461-471.
34. Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins 2007; 69: 511-520.
35. Sundberg EJ, Sawicki MW, Southwood S, Andersen PS, Sette A, Mariuzza RA. Minor structural changes in a mutated human melanoma antigen correspond to dramatically enhanced stimulation of a CD4+ tumor-infiltrating lymphocyte line. J Mol Biol 2002; 319: 449-461.
36. Sokal RR, Michener CD. A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 1958; 38: 1409-1438.
37. Lloyd SP. Least square quantization in PCM. IEEE Trans Inform Theory 1982; 28: 129-137.
38. Kent HM, Moore MS, Quimby BB, Baker AM, McCoy AJ, Murphy GA, Corbett AH, Stewart M. Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import. J Mol Biol 1999; 289: 565-577.
39. Bullock TL, Clarkson WD, Kent HM, Stewart M. The 1.6 angstroms resolution crystal structure of nuclear transport factor 2 (NTF2). J Mol Biol 1996; 260: 422-431.
40. Chen R, Weng ZP. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002; 47: 281-294.
41. Chen R, Weng ZP. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003; 51: 397-408.
42. Takemura K, Guo H, Sakuraba S, Matubayasi N, Kitao A. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation. J Chem Phys 2012; 137: 215105.
43. Matubayasi N, Nakahara M. Theory of solutions in the energetic representation. I. Formulation. J Chem Phys 2000; 113: 6070-6081.
44. Matubayasi N, Nakahara M. Theory of solutions in the energy representation. II. Functional for the chemical potential. J Chem Phys 2002; 117: 3605-3616; J Chem Phys 118(2003)2446 (erratum).
45. Matubayasi N, Nakahara M. Theory of solutions in the energy representation. III. Treatment of the molecular flexibility. J Chem Phys 2003; 119: 9686-9702.
46. Jorgensen R, Ortiz PA, Carr-Schmid A, Nissen P, Kinzy TG, Andersen GR. Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase. Nat Struct Biol 2003; 10: 379-385.
47. Yates SP, Taylor PL, Jorgensen R, Ferraris D, Zhang J, Andersen GR, Merrill AR. Structure-function analysis of water-soluble inhibitors of the catalytic domain of exotoxin A from Pseudomonas aeruginosa. Biochem J 2005; 385(Part 3): 667-675.
48. Volz K, Matsumura P. Crystal structure of Escherichia coli CheY refined at 1.7-A resolution. J Biol Chem 1991; 266: 15511-15519.
49. McEvoy MM, Muhandiram DR, Kay LE, Dahlquist FW. Structure and dynamics of a CheY-binding domain of the chemotaxis kinase CheA determined by nuclear magnetic resonance spectroscopy. Biochemistry 1996; 35: 5633-5640.
50. Lee TW, James MNG. 1.2 angstrom-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB). BBA-Proteins Proteom 2008; 1784: 319-334.
51. Bode W, Epp O, Huber R, Laskowski M, Ardelt W. The Crystal and molecular-structure of the 3rd domain of silver pheasant ovomucoid (Omsvp3). Eur J Biochem 1985; 147: 387-395.