Prediction of protein-ligand complex structure by docking software guided by other complex structures

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 6, 2008, Pages 1030-1033

  Fukunishi, Yoshifumi ^a,b   Nakamura, Haruki ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Pharmaceutical Innovation Value Chain   (Japan)

^c OSAKA UNIVERSITY   (Japan)

Author keywords

Docking score; Protein ligand complex; Protein ligand docking

Indexed keywords

COMPUTER SOFTWARE; INFORMATION ANALYSIS; PROTEINS;

DOCKING PROGRAMS; DOCKING SOFTWARES; PROTEIN LIGAND DOCKINGS; STRUCTURAL INFORMATIONS;

LIGANDS;

ACCURACY; ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; ENERGY; ENTROPY; GEOMETRY; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN BINDING;

BINDING SITES; LIGANDS; PREDICTIVE VALUE OF TESTS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 37349040712     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.07.001     Document Type: Article

References (20)

1. Warren G.L., Andrews C.W., Capelli A.M., Clarke B., LaLonde J., Lambert M.H., Lindvall M., Nevins N., Semus S.F., Senger S., Tedesco G., Wall I.D., Woolven J.M., Peishoff C.E., and Head M.S. A critical assessment of docking programs and scoring functions. J. Med. Chem. 49 (2006) 5912-5931
2. Kontoyianni M., Sokol G.S., and McClellan L.M. Evaluation of library ranking efficacy in virtual screening. J. Comput. Chem. 26 (2005) 11-22
3. Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., and Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161 (1982) 269-288
4. Rarey M., Kramer B., Lengauer T., and Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261 (1996) 470-489
5. Jones G., Willet P., Glen R.C., Leach A.R., and Taylor R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267 (1997) 727-748
6. Baxter C.A., Murray C.W., Clark D.E., Westhead D.R., and Eldridge M.D. Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 33 (1998) 367-382
7. Fukunishi Y., Mikami Y., and Nakamura H. Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening. J. Mol. Graph. Model. 24 (2005) 34-45
8. Zhang C., Liu S., Zhu Q., and Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 48 (2005) 2325-2335
9. Muegge I., and Martin Y.C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 42 (1999) 791-804
10. Vigers G.P.A., and Rizzi J.P. Multiple active site corrections for docking and virtual screening. J. Med. Chem. 47 (2004) 80-89
11. Fukunishi Y., Mikami Y., Kubota S., and Nakamura H. Multiple target screening method for robust and accurate in silico ligand screening. J. Mol. Graph. Model. 25 (2005) 61-70
12. Fukunishi Y., Kubota S., and Nakamura H. Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening. J. Chem. Inf. Model. 46 (2006) 2071-2084
13. Kearsley S.K. On the orthogonal transformation used for structural comparisons. Acta Crystallogr. A45 (1989) 208-210
14. Gasteiger J., and Marsili M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 36 (1980) 3219-3228
15. Gasteiger J., and Marsili M. A new model for calculating atomic charges in molecules. Tetrahedron Lett. (1978) 3181-3184
16. Case D.A., Darden T.A., Cheatham III T.E., Simmerling C.L., Wang J., Duke R.E., Luo R., Merz K.M., Wang B., Pearlman D.A., Crowley M., Brozell S., Tsui V., Gohlke H., Mongan J., Hornak V., Cui G., Beroza P., Schafmeister C., Caldwell J.W., Ross W.S., and Kollman P.A. Amber 8 (2004), UCSF
17. McGovern S.L., and Shoichet B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 46 (2003) 2895-2907
18. Paul N., and Rognan D. ConsDock: a new program for the consensus analysis of protein-ligand interactions. Protein Struct. Funct. Genet. 47 (2002) 521-533
19. Nissink J.W.M., Murray C., Hartshorn M., Verdonk M.L., Cole J.C., and Taylor R. A new test set for validating predictions of protein-ligand interaction. Protein Struct. Funct. Genet. 49 (2002) 457-471
20. Bunke H., and Shearer K. A graph distance metric based on the maximal common subgraph. Pattern Recognit. Lett. 19 (1998) 255-259