Evaluation of ligand-binding affinity using polynomial empirical scoring functions

Bioorganic and Medicinal Chemistry

Volumn 16, Issue 20, 2008, Pages 9378-9382

  de Azevedo Jr , Walter Filgueira ^a   Dias, Raquel ^a  

^a PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Docking; Empirical scoring functions; Protein ligand; Virtual screening

Indexed keywords

ARTICLE; BINDING AFFINITY; COMPUTER PROGRAM; HYDROGEN BOND; INTERMETHOD COMPARISON; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR INTERACTION; SCORING SYSTEM;

EMPIRICAL RESEARCH; HYDROGEN BONDING; LIGANDS; MODELS, BIOLOGICAL; SURFACE PROPERTIES;

EID: 53249117061     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2008.08.014     Document Type: Article

References (27)

1. Böhm H.-J., and Schneider G. Protein-Ligand Interactions (2003), WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany
2. Gilson M.K., and Zhou H.X. Annu. Rev. Biophys. Biomol. Struct. 36 (2007) 21
3. Salazar P.F., and Seminário J. Phys. Chem. B 112 (2008) 1290
4. Böhm H.-J.J. Comput.-Aided Mol. Des. 8 (1994) 243
5. Rajamani R., and Good A.C. Curr. Opin. Drug Discov. Dev. 10 (2007) 308
6. Laurie A.T., and Jackson R.M. Curr. Protein Pept. Sci. 7 (2006) 395
7. Vajda S., and Guarnieri F. Curr. Opin. Drug Discov. Dev. 9 (2006) 354
8. Cozzini P., Fornabaio M., Marabotti A., Abraham D.J., Kellogg G.E., and Mozzarelli A. Curr. Med. Chem. 11 (2004) 3093
9. Wang R., Lai L., and Wang S.J. Comput.-Aided Mol. Des. 16 (2002) 11
10. Krammer A., Kirchhoff P.D., Jiang X., Venkatachalam C.M., and Waldman M. J. Mol. Graph. Model. 23 (2005) 395
11. Caceres R.A., Timmers L.F.M.S., Dias R., Basso L.A., Santos D.S., and de Azevedo W.F. Bioorg. Med. Chem. 9 (2008) 4984
12. Wallace A.C., Laskowski R.A., and Thornton J.M. Protein Eng. 8 (1995) 127
13. Rizzo R.C., Udier-Blagovic M., Wang D.P., Watkins E.K., Kroeger Smith M.B., Smith R.H., Tirado-Rives J., and Jorgensen W.L.J. Med. Chem. 45 (2002) 2970
14. Mark A.E., and van Gunsteren W.F. J. Mol. Biol. 240 (1994) 167
15. Williams D.H., and Bardsley B. Perspect. Drug Discov. Design. 17 (1999) 43
16. Wang R., Lu Y., Fang X., and Wang S.J. Chem. Inf. Comput. Sci. 44 (2004) 2114
17. Boehm H.-J., and Klebe G. Angew. Chem. Int. Ed. 35 (1996) 2589
18. Matsumara M., Matthews B.W., and Beckel W.J. Nature 334 (1988) 406
19. Nauchatel V., Villaverde M.C., and Sussman F. Protein Sci. 4 (1995) 1356
20. Collaborative Computational Project, Number 4. Acta Cryst. 1994, D50, 760.
21. De Azevedo W.F., Mueller-Dieckmann H.J., Schulze-Gahmen U., Worland P.J., Sausville E., and Kim S.-H. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 2735
22. De Azevedo W.F., Leclerc S.J., Meijer L., Havlicek L., Strnad M., and Kim S.H. Eur. J. Biochem. 243 (1997) 518
23. De Azevedo W.F., Canduri F., Fadel V., Teodoro L.G., Hial V., and Gomes R.A. Biochem. Biophys. Res. Comm. 287 (2001) 277
24. Latimer W.M., and Rodebush W.H. J. Am. Chem. Soc. 2 (1920) 1419
25. Jeffrey G.A. An Introduction to Hydrogen Bonding (1997), Oxford University Press, Oxford University
26. Huggins M.L. Angew. Chem. Int. Ed. 10 (1971) 147
27. Wang R., Lu Y., and Wang S. J. Med. Chem. 46 (2003) 2287