SOFTDOCK application to protein-protein interaction benchmark and CAPRI

Proteins: Structure, Function and Genetics

Volumn 69, Issue 4, 2007, Pages 801-808

  Li, Nan ^a,b   Sun, Zhonghua ^a,b   Jiang, Fan ^a  

^a INSTITUTE OF PHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Biological complex; Coarse grained algorithm; Conformational change; Electrostatic interaction; Global search; Grid based scoring; Molecular docking; Shape complementarity; Voronoi surface

Indexed keywords

ARGININE; DOCKING PROTEIN; LYSINE;

COMPLEX FORMATION; CONFERENCE PAPER; ENERGY CONSERVATION; GEOMETRY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; ELECTROSTATICS; GENOMICS; LIGANDS; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 36749072540     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21728     Document Type: Conference Paper

References (43)

1. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davery M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso SR, Onge PS, Ghanny S, Lam MH, Butland G, Altaf-UI AM, Kanaya S, Shilatifard A, O'shea Weissman JS, Ingles CJ, Heghes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006;440:637-643.
2. Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature 2003;422;208-215.
3. Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics. Nature 2003;422:216-225.
4. Smith JR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
5. Deremble C, Lavery R. Macromolecular recognition. Curr Opin Struct Biol 2005;15:171-175.
6. Jiang F, Kim SH. "Soft docking": matching of molecular surface cubes. J Mol Biol 1991;219:79-102.
7. Jiang F, Lin W, Rao ZH. SOFTDOCK: understanding of molecular recognition through a systematic docking study. Protein Eng 2002;15:257-263.
8. Cherfils J, Duouerroy S, Janin J. Protein-protein recognition analyzed by docking simulation. Proteins 1991;11:271-280.
9. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vasker 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.
10. Vakser IA. Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction. Protein Eng 1996;9:37-41.
11. Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
12. 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.
13. Abgagyan 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 Comp Chem 1994;15:488-506.
14. Abgagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and protein. J Mol Biol 1994;235:983-1002.
15. Fernandez-redo J, Totrov M, Abgagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
16. Fernandez-recio J, Totrov M, Abgagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
17. Fernandez-recio J, Totrov M, Abgagyan R. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 2005;60:308-313.
18. Fernandez-recio J, Totrov M, Skorodumov C, Abgagyan R. Optimal docking area: a new method for predicting protein-protein interaction site. Proteins 2005;58:134-143.
19. Chen R, Li L, Weng ZP. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
20. Chen R, Weng ZP. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
21. Chen R, Weng ZP. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
22. 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.
23. Smith GR, Fitzjohn PW, Page CS, Bates PA. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 2005;60:263-268.
24. 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.
25. Janin J, Henrick K, Moult J, Eyck JT, Sternberg MJ, Vajda S, Vasker IA, Wodak SJ. CAPRI: a critical assessment of predicted interactions. Proteins 2003;52:2-9.
26. Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
27. Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH. Molecular basis for bacterial class I release factor methylation by PrmC. Mol Cell 2005;20:917-927.
28. Hou Z, Bernstein DA, Fox CA, Keck JL. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 2005;102:8489-8494.
29. Nielsen TK, Liu S, Luhrmann R, Ficner R. Structural basis for the bifunctionality of the U5 snRNP 52K protein (CD2BP2). J Mol Biol 2007;369:902-908.
30. Ghosh A, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C. How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Nature 2006;440:101-104.
31. 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.
32. Grishkovskaia I, Bonsor DA, Kleanthous C, Dodson EJ. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
33. Walker JR, Avvakumov GV, Xue S, Newman EM, Mackenzie F, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon S. A novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa, to be published.
34. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng ZP. Protein-Protein docking benchmark 2.0: an update. Proteins 2005;60:214-216.
35. Gerstein M, Tsai J, Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol 1995;249:955-966.
36. Rocchia W, Alexov E, Honig B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B 2001;105:6507-6514.
37. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J Comp Chem 2002;23:128-137.
38. Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Homak V, Cui G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman PA. Amber8. University of California, San Francisco; 2004.
39. Kowalsman N, Eisenstein M. Inherent limitations in protein-protein docking procedures. Bioinformatics 2007;29:421-426.
40. Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343
41. Bahadur RP, Chakrabarti P, Rodier F, and Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
42. Jackson RM. Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. Protein Sci 1999;8:603-613.
43. Bernauer J, Aze J, Janin J, Poupon A. A new protein-protein docking scoring function based on interface residue properties. Bioinformatics 2007;23:555-562.