A branch-and-bound method for optimal atom-type assignment in de novo ligand design

Journal of Computer-Aided Molecular Design

Volumn 12, Issue 4, 1998, Pages 335-

  Todorov, N P ^a   Dean, P M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Drug design; Free energy; Molecular design; Protein ligand interaction; Structure generation

Indexed keywords

ATOMS; BINDING ENERGY; BRANCH AND BOUND METHOD; COMPLEXATION; LIGANDS; MUSCULOSKELETAL SYSTEM; PROTEINS;

BRANCH-AND-BOUND METHODS; COMPUTATIONAL PROCEDURES; DE NOVO LIGAND DESIGNS; DRUG DESIGN; IONIZATION STATE; MOLECULAR DESIGN; MOLECULAR SKELETON; PROTEIN-LIGAND INTERACTIONS; RECEPTOR SITES; STRUCTURE GENERATION;

FREE ENERGY;

DIHYDROFOLATE REDUCTASE; LIGAND; PROTEINASE; RETINOL BINDING PROTEIN; THERMOLYSIN; TRYPSIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DESIGN; THERMODYNAMICS;

ALGORITHMS; BINDING SITES; COMPUTER-AIDED DESIGN; DRUG DESIGN; HIV PROTEASE; LIGANDS; MOLECULAR STRUCTURE; RETINOL-BINDING PROTEINS; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS; THERMOLYSIN; TRYPSIN;

EID: 0032111471     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1007994827087     Document Type: Article

References (35)

1. Slater, P.E. and Timms, D., J. Mol. Graph., (1993) 248.
2. Verlinde, C.L.M.J. and Hol, W.G.J., Structure, 2 (1994) 577.
3. Lewis, R.A. and Leach, A.R., J. Comput.-Aided Mol. Design, 8 (1994) 467.
4. Lewis, R.A. and Dean, P.M., Proc. R. Soc. London, B236 (1989) 125.
5. Lewis, R.A. and Dean, P.M., Proc. R. Soc. London, B236 (1989) 141.
6. Todorov, N.P. and Dean, P.M., J. Comput.-Aided Mol. Design, 11 (1997) 175.
7. Chan, S.L., Chau, P.-L. and Goodman, J.M., J. Comput.-Aided Mol. Design, 6 (1992) 461.
8. Nakamura, H., Komatsu, K., Nakagawa, S. and Umeyana, H., J. Mol. Graph., 3 (1985) 2.
9. Chau, P.-L. and Dean, P.M., J. Comput.-Aided Mol. Design, 8 (1994) 513.
10. Chau, P.-L. and Dean, P.M., J. Comput.-Aided Mol. Design, 8 (1994) 527.
11. Chau, P.-L. and Dean, P.M., J. Comput.-Aided Mol. Design, 8 (1994) 545.
12. Barakat, M.T. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 341.
13. Barakat, M.T. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 351.
14. Barakat, M.T. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 359.
15. Barakat, M.T. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 448.
16. Barakat, M.T. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 457.
17. Chau, P.-L. and Dean, P.M., J. Comput.-Aided Mol. Design, 6 (1992) 385.
18. Chau, P.-L. and Dean, P.M., J. Comput.-Aided Mol. Design, 6 (1992) 397.
19. Chau, P.-L. and Dean, P.M., J. Comput.-Aided Mol. Design, 6 (1992) 407.
20. Gullet, V., Johnson, A.P., Mata, P., Sike, S. and Zsoldos, Z., J. Comput.-Aided Mol. Design, 7 (1993) 127.
21. Gillet, V., Newell, W., Mata, P., Myatt, G., Sike, S., Zsoldos, Z. and Johnson, A.P., J. Comput.-Aided Mol. Design, 7 (1993) 127.
22. Böhm, H.-J., J. Comput.-Aided Mol. Design, 8 (1994) 243.
23. Gray, N.A.B., Computer-Assisted Structure Elucidation, Chapter XI, pp. 399-455, John Wiley and Sons, New York, NY, 1986.
24. Morley, S.D., Abraham, R.J., Haworth, I.S., Jackson, D.E., Saunders, M.R. and Vinter, J.G., J. Comput.-Aided Mol. Design, 5 (1991) 475.
25. Nilsson, N.J., Principles of Artificial Intelligence, Springer-Verlag, Berlin, 1982.
26. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
27. Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T., Numerical Recipes: The Art of Scientific Computing, Cambridge University Press, Cambridge, 1986.
28. Marquart, M., Walter, J., Deisenhofer, J., Bode, W., Huber, R., Acta Crystallogr. B, 39 (1983) 480.
29. Mares-Guia, M. and Shaw, E., J. Biol. Chem., 240 (1965) 1579.
30. Cowan, S.W., Newcomer, M.E. and Jones, T.A., Proteins, 8 (1990) 44.
31. Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. and Kraut, J., J. Biol. Chem., 257 (1982) 13650.
32. Matthews, B.W., Acc. Chem. Res., 21 (1988) 333.
33. Bone, R., Vacca, J.P., Anderson, P.S. and Holloway, M.K., J. Am. Chem. Soc., 113 (1991) 9382.
34. Dean, P.M., In Dean, P.M. (Ed.) Molecular Similarity in Drug Design, pp. 1-23, Blackie Academic and Professional, Cambridge, 1995.
35. Ihlenfeldt, W.D., Takahashi, Y., Abe, H. and Sasaki, S., J. Chem. Inf. Comput. Sci., 34 (1982) 109.