GRAMM-X public web server for protein-protein docking

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Tovchigrechko, Andrey ^a   Vakser, Ilya A ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING PROTEIN; LIGAND; MULTIPROTEIN COMPLEX;

ARTICLE; CLIENT SERVER APPLICATION; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; FOURIER TRANSFORMATION; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; EVALUATION; METABOLISM;

BINDING SITES; COMPUTATIONAL BIOLOGY; INTERNET; LIGANDS; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33747840389     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl206     Document Type: Article

References (18)

1. Katchalski-Katzir,E., Shariv,I., Eisenstein,M., Friesem,A.A., Aflalo,C. and Vakser,I.A. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl Acad. Sci. USA, 89, 2195-2199.
2. Vakser,I.A. and Aflalo,C. (1994) Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins, 20, 320-329.
3. Vakser,I.A. (1995) Protein docking for low-resolution structures. Protein Eng., 8, 371-377.
4. Marshall,G.R. and Vakser,I.A. (2005) Protein-protein docking methods. In Waksman,G. (ed.), Proteomics and Protein-Protein Interaction: Biology, Chemistry, Bioinformatics, and Drug Design. Springer, NY, pp. 115-146.
5. Tovchigrechko,A. and Vakser,I.A. (2005) Development and testing of an automated approach to protein docking. Proteins, 60, 296-301.
6. Vakser,I.A. (1996) Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction. Protein Eng., 9, 37-41.
7. 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.
8. Tovchigrechko,A. and Vakser,I.A. (2001) How common is the funnel-like energy landscape in protein-protein interactions? Protein Sci., 10, 1572-1583.
9. Jiang,S., Tovchigrechko,A. and Vakser,I.A. (2003) The role of geometric complementarity in secondary structure packing: a systematic docking study. Protein Sci., 12, 1646-1651.
10. Schafer,H., Van Gunsteren,W.F. and Mark,A.E. (1999) Estimating relative free energies from a single ensemble: hydration free energies. J. Comput. Chem., 20, 1604-1617.
11. Chen,R., Mintseris,J., Janin,J. and Weng,Z. (2003) A protein-protein docking benchmark. Proteins, 52, 88-91.
12. Comeau,S.R., Gatchell,D.W., Vajda,S. and Camacho,C.J. (2004) ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20, 45-50.
13. Schneidman-Duhovny,D., Inbar,Y., Nussinov,R. and Wolfson,H.J. (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res., 33, W363-W367.
14. Daily,M.D., Masica,D., Sivasubramanian,A., Somarouthu,S. and Gray,J.J. (2005) CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins, 60, 181-186.
15. Terashi,G., Takeda-Shitaka,M., Takaya,D., Komatsu,K. and Umeyama,H. (2005) Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues. Proteins, 60, 289-295.
16. Camacho,C.J. (2005) Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins, 60, 245-251.
17. Wiehe,K., Pierce,B., Mintseris,J., Tong,W., Anderson,R., Chen,R. and Weng,Z. (2005) ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins, 60, 207-221.
18. Mandell,J.G., Roberts,V.A., Pique,M.E., Kotlovyi,V., Mitchell,J.C. and Nelson,E. (2001) Tsigelny I and Ten Eyck LF, Protein docking using continuum electrostatics and geometric fit. Protein Eng., 14, 105-113.