A new method for predicting binding affinity in computer-aided drug design

Protein Engineering, Design and Selection

Volumn 7, Issue 3, 1994, Pages 385-391

  Åqvist, Johan ^a   Medina, Carmen ^a,b   Samuelsson, Jan Erik ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b Symbicom AB ^*  (Sweden)

Author keywords

Binding free energies; Drug design; Endothiapepsin; Inhibitor binding; Molecular dynamics simulation

Indexed keywords

ENDOTHIAPEPSIN; ENZYME INHIBITOR; PEPTIDE HYDROLASE;

ARTICLE; BINDING AFFINITY; COMPUTER AIDED DESIGN; COMPUTER MODEL; CONTROLLED STUDY; DRUG DESIGN; ENTHALPY; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; THERMODYNAMICS;

ASPARTIC ENDOPEPTIDASES; BINDING SITES; COMPUTER SIMULATION; DRUG DESIGN; ELECTROCHEMISTRY; MOLECULAR STRUCTURE; PROTEIN BINDING; SUPPORT, NON-U.S. GOV'T; THERMODYNAMICS;

EID: 0028155689     PISSN: 17410126     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/7.3.385     Document Type: Article

References (37)

1. Åqvist, I. (1990) J. Phys. Chem., 94, 8021-8024.
2. Åqvist, J., Fothergill, M. and Warshel, A. (1993) J. Am. Chem. Soc., 115, 631-635.
3. Bash, P.A., Singh, U.C., Brown, F.K., Langridge, R. and Kollman, P.A. (1987) Science, 235, 574-576.
4. Ben-Naim, A. and Marcus, Y. (1984) J. Chem. Phys., 81, 2016-2027.
5. Beveridge, D.L. and DiCapua, F.M. (1989) Amm. Rev. Biophys. Biophys. Chem., 18, 431-492.
6. Brooks, C.L., III (1989) In van Gunstercn, W.F. and Weiner, P.K. (eds), Computer Simulation of Biomolecular Systems. ESCOM, Leiden, pp. 73-88.
7. Chandler, D., Weeks, J.D. and Andersen, H.C. (1983) Sciaice, 220, 787-794.
8. Cohen, N.C., Blaney, J.M., Humblet, C., Gund, P. and Barry, D.C. (1990) J. Med Chem., 33, 883-894.
9. Davies, D.R. (1990) Annu. Rev. Biophys. Biophys. Chem., 19, 189-215.
10. Dixon, J.S. (1992) TIBTECH, 10, 357-363.
11. Foundling, S.I., Cooper, J., Watson, F.E., Cleasby, A., Peari, L.H., Sibanda, B.L., Hemmings, A., Wood, S.P., Blundell, T.L., Valler, M.J., Norey, C.G., Kay, J., Boger, J., Dunn, B.M., Leckie, B.J., Jones, D.M., Atrash, B., Hallett, A. and Szelke, M. (1987) Nature, 327, 349-352.
12. Fruton, J.S. (1976) Adv. Enzymol, 44, 1-36.
13. Hubbard, R.E. (1984) In The Representation of Protein Structure, Proc. Computer-Aided Molecular Design Conference, Oyez, New York, p. 99.
14. Jones, T.A. (1978) J. Appl Crystal, 11, 268-272.
15. Jorgensen, W.L. (1986) J. Phys. Chem., 90, 1276-1284.
16. Jorgensen, W.L. (1989) Acc. Chem. Res., 22, 184-189.
17. King, G. and Warshel, A. (1990) J. Chem. Phys., 93, 8682-8692.
18. Lee, F.S., Chu, Z.-T., Bolger, M.B. and Warshel, A. (1992) Protein Engng, 5, 215-228.
19. Marcus, R.A. (1964) Ann. Rev. Phys. Chem., 15, 155-196.
20. McDonald, J. and Brooks, C.L., III. (1991) J. Am. Chem. Soc., 113, 2295-2301.
21. Merz, K.M. JT and Kollman, P.A. (1989) J. Am. Chem. Soc., 111, 5649-5658.
22. Meiz, K.M., Jr, Murcko, M.A. and Kollman, P.A. (1991) J. Am. Chem. Soc., 113, 4484-4490.
23. Mitchell, M.J. and McCammon, J.A. (1991) J. Comput. Chem., 12, 271-275.
24. Pearlman, D.A. and Kollman, P.A. (1991) J. Chem. Phys., 94, 4532-4545.
25. Pratt, L.R. and Chandler, D. (1977) J. Chem. Phys., 67, 3683-3704.
26. Rao, B.G. and Singh, U.C. (1991) J. Am. Chem. Soc., 113, 6735-6750.
27. Roux, B., Yu, H.-A. and Kaiplus, M. (1990) J. Phys. Chem., 94, 4683-4688.
28. Straatsma, T.P. and Berendsen, H.J.C. (1988) J. Chem. Phys., 89, 5876-5886.
29. Straatsma, T.P. and McCammon, J.A. (1991) J. Chem. Phys., 95, 1175-1188.
30. Straatsma, T.P. and McCammon, J.A. (1992) Ann. Rev. Phys. Chem., 43, 407-435.
31. Tropsha, A. and Hermans, T. (1992) Protein Engng, 5, 29-33.
32. van Gunsteren, W.F. and Berendsen, H.J.C. (1987) Groningen Molecular Simulation (GROMOS) Library Manual. Biomos BV, Nijenborgh 16, Groningen, The Netherlands.
33. Veerapandian, B., Cooper, J.B., Sali, A. and Blundell, T.L. (1990) J. Mol Biol., 216, 1017-1029.
34. Warshel, A. and Russell, S.T. (1984) Q. Rev. Biophys., 17, 283-422.
35. Warshel, A. and Creighton, S. (1989) In van Gunsteren, W.F. and Weiner, P.K. (eds), Computer Simulation of Biomolecular Systems. ESCOM, Leiden, pp. 120-138.
36. Wong, C.F. and McCammon, J.A. (1986) J. Am. Chem. Soc., 108, 3830-3832.
37. Zwanzig, R.W. (1954) J. Chem Phys., 22, 1420-1426.