PatchDock and SymmDock: Servers for rigid and symmetric docking

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Schneidman Duhovny, Dina ^a   Inbar, Yuval ^a   Nussinov, Ruth ^a,b   Wolfson, Haim J ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLIENT SERVER APPLICATION; COMPUTER PREDICTION; INTERNET; METHODOLOGY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; WEB BROWSER; ALGORITHM; COMPUTER INTERFACE; COMPUTER PROGRAM; GEOMETRY; MOLECULAR DYNAMICS; PREDICTION; PROTEIN DATABASE; CHEMISTRY; PROTEIN CONFORMATION;

PROTEIN; LIGAND; MULTIPROTEIN COMPLEX;

ALGORITHMS; INTERNET; LIGANDS; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 21644476468     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki481     Document Type: Article

References (28)

1. Katchalski-Katzir,E., Shariv,I., Eisenstein,M., Friesem,A., Aflalo,C. and Vakser,I. (1992) Molecular surface recognition: Determination of geometric fit between protein and their ligands by correlation techniques. Proc. Natl Acad. Sci. USA, 89, 2195-2199.
2. Kuntz,I., Blaney,J., Oatley,S., Langridge,R. and Ferrin,T. (1982) A geometric approach to macromolecule-ligand interactions. J. Mol. Biol., 161, 269-288.
3. Connolly,M.L. (1986) Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface. Biopolymers, 25, 1229-1247.
4. Jiang,F. and Kim,S. (1991) "Soft docking": Matching of molecular surface cubes. J. Mol. Biol., 219, 79-102.
5. Walls,P. and Sternberg,M. (1992) New algorithms to model protein-protein recognition based on surface complementarity; applications to antibody-antigen docking. J. Mol. Biol., 228, 227-297.
6. Norel,R., Lin,S., Wolfson,H.J. and Nussinov,R. (1994) Shape complementarity at protein-protein interfaces. Biopolymers, 34, 933-940.
7. Fischer,D., Lin,S., Wolfson,H.J. and Nussinov,R. (1995) A geometry-based suite of molecular docking processes. J. Mol. Biol., 248, 459-477.
8. Vakser,I. (1995) Protein docking for low-resolution structures. Protein Eng., 8, 371-377.
9. Vakser,I. (1996) Main-chain complementarity in protein-protein recognition. Protein Eng., 9, 741-744.
10. Althaus,E., Kohlbacher,O., Lenhof,H. and Müller,P. (2002) A combinatorial approach to protein docking with flexible side chains. J. Comput. Biol., 9, 597-612.
11. Jones,G., Willet,P., Glen,R.C., Leach,A.R. and Taylor,R. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267, 727-748.
12. Vakser,I.A., Matar,O.G. and Lam,C.F. (1999) A systematic study of low-resolution recognition in protein-protein complexes. Proc. Natl Acad. Sci. USA, 96, 8477-8482.
13. Gabb,H.A., Jackson,R.M. and Sternberg,M.J. (1997) Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J. Mol. Biol., 272, 106-120.
14. Camacho,C.J., Gatchell,D.W., Kimura,S.R. and Vajda,S. (2000) Scoring docked conformations generated by rigid-body protein-protein docking. Proteins, 40, 525-537.
15. Goldman,B.B. and Wipke,W.T. (2000) QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock). Proteins, 38, 79-94.
16. Gardiner,E.J., Willett,P. and Artymiuk,P.J. (2001) Protein docking using a genetic algorithm. Proteins, 44, 44-56.
17. Chen,R. and Weng,Z. (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47, 281-294.
18. Gay,J.J., Moughon,S., Wang,C., Schueler-Furman,O., Kuhlman,B., Rohl,C.A. and Baker,D. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol., 331, 281-299.
19. Comeau,S.R., Gatchell,D.W., Vajda,S. and Camacho,C.J. (2004) ClusPro: A fully automated algorithm for protein-protein docking. Nucleic Acids Res., 32, W96-W99.
20. Duhovny,D., Nussinov,R. and Wolfson,H.J. (2002) Efficient unbound docking of rigid molecules. In Guigo,R. and Gusfield,D. (eds), Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics. Springer-Verlag GmbH Rome, Italy, September 17-21, 2002, Vol. 2452, pp. 185-200.
21. Chen,R., Mintseris,J., Janin,J. and Weng,Z. (2003) A protein-protein docking benchmark. Proteins, 52, 88-91.
22. Inbar,Y., Schneidman-Duhovny,D., Halperin,I., Oron,A., Nussinov,R. and Wolfson,H.J. (2005) Approaching the CAPRI challenge with efficient geometry based docking. Proteins (in press).
23. Schneidman-Duhovny,D., Inbar,Y., Nussinov,R. and Wolfson,H.J. (2005) Geometry based flexible and symmetric protein docking. Proteins (in press).
24. Eisenstein,M., Shariv,I., Koren,G., Friesem,A.A. and Katchalski-Katzir,E. (1997) Modeling supra-molecular helices: Extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus. J. Mol. Biol., 266, 135-143.
25. Berchanski,A. and Eisenstein,M. (2003) Construction of molecular assemblies via docking: Modeling of tetramers with D2 symmetry. Proteins, 53, 817-829.
26. Connolly,M.L. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709-713.
27. Connolly,M.L. (1983) Analytical molecular surface calculation. J. Appl. Crystallogr., 16, 548-558.
28. Zhang,C., Vasmatzis,G., Cornette,J.L. and DeLisi,C. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol., 267, 707-726.