A Monte Carlo method for finding important ligand fragments from receptor data

Journal of Computer-Aided Molecular Design

Volumn 11, Issue 3, 1997, Pages 243-255

  Burt, Stan ^a   Hutchins, Charles ^b   Zielinski, Peter J ^c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b ABBOTT LABORATORIES   (United States)

^c D9P9 AP32   (United States)

Author keywords

Ligand design; Rational ligand design; Simulated annealing; Structure based ligand design

Indexed keywords

BOLTZMANN EQUATION; MONTE CARLO METHODS; SIMULATED ANNEALING;

LIGAND DESIGN; MONTECARLO METHODS; POLARIZATION ENERGY; RATIONAL LIGAND DESIGN; RECEPTOR CAVITIES; SIMULATED ANNEALING METHOD; STRUCTURE-BASED; STRUCTURE-BASED LIGAND DESIGN;

LIGANDS;

LIGAND; SIALIC ACID DERIVATIVE; SIALIDASE; SOLVENT;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; MONTE CARLO METHOD; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; MONTE CARLO METHOD; NEURAMINIDASE; PROTEIN STRUCTURE, TERTIARY; SIALIC ACIDS; SOLVENTS; THERMODYNAMICS;

EID: 0031135808     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1007952511172     Document Type: Article

References (46)

1. Andrews, P., In Foye, W. (Ed.) Principles of Medicinal Chemistry, 3rd ed., Lea & Febiger, Philadelphia, PA, U.S.A., 1990, pp. 855-860.
2. Bugg, C., Carson, W. and Montgomery, J., Sci. Am., 269 (1993) 92.
3. Von Itzstein, M., Wu, W., Kok, G., Pegg, M., Dyason, J., Jin, B., Pahn, T., Smythe, M., White, H., Oliver, S., Colman, P., Varghese, J., Ryan, M., Woods, J., Bethell, R., Hotham, V., Cameron, J. and Penn, C., Nature, 363 (1993) 418.
4. Kuntz, I., Blaney, J., Oatley, S., Langridge, R. and Ferrin, T., J. Mol. Biol., 161 (1982) 269.
5. DesJarlais, R., Sheridan, R., Seibel, J., Dixon, S., Kuntz, I. and Venkataraghavan, R., J. Med. Chem., 31 (1988) 722.
6. Martin, Y., J. Med. Chem., 35 (1992) 2145.
7. Rotstein, S. and Murcko, M., J. Med. Chem., 36 (1993) 1700.
8. Namasivayam, S. and Dean, P., J. Mol. Graph., 4 (1986) 46.
9. Lewis, R., Roe, D., Huang, C., Ferrin, T., Langridge, R. and Kuntz, I., J. Mol. Graph., 10 (1992) 66.
10. Kato, Y., Akiko, I. and Iitaka, Y., Tetrahedron, 43 (1987) 5229.
11. Meng, E., Shoichet, B. and Kuntz, I., J. Comput. Chem., 13 (1992) 505.
12. Karfunkel, H., J. Comput. Chem., 7 (1986) 113.
13. DesJarlais, R., Sheridan, R., Dixon, S., Kuntz, I. and Venkataraghavan, R., J. Med. Chem., 29 (1986) 2149.
14. Billeter, M., Havel, T. and Kuntz, I., Biopolymers, 26 (1987) 777.
15. Goodsell, D. and Olson, A., Proteins, 8 (1990) 195.
16. Hart, T. and Read, R., Proteins, 13 (1992) 206.
17. Goodford, P., J. Med. Chem., 28 (1985) 849.
18. Boobbyer, D., Goodford, P., McWhinni, P. and Wade, R., J. Med. Chem., 32 (1989) 1083.
19. Wade, R., Clark, K. and Goodford, P., J. Med. Chem., 36 (1993) 140.
20. Wade, R. and Goodford, P., J. Med. Chem., 36 (1993) 148.
21. Kellogg, G. and Abraham, D., J. Mol. Graph., 10 (1992) 212.
22. Miranker, A. and Karplus, M., Proteins, 1 (1991) 29.
23. Caflisch, A., Miranker, A. and Karplus, M., J. Med. Chem., 35 (1993) 2142.
24. Gillet, V., Johnson, P., Mata, P., Sike, S. and Williams, P., J. Comput.-Aided Mol. Design, 7 (1993) 127.
25. Nishibata, Y. and Akiko, I., Tetrahedron, 47 (1991) 8985.
26. Nishibata, Y. and Akiko, I., J. Med. Chem., 36 (1993) 2921.
27. Lawrence, M. and Davis, P., Proteins Struct. Funct. Genet., 12 (1992) 31.
28. Böhm, H.-J., J. Comput.-Aided Mol. Design, 6 (1992) 61.
29. Eisen, M., Wiley, D., Karplus, M. and Hubbard, R., Proteins Struct. Funct. Genet., 19 (1994) 199.
30. Lewis, R., J. Comput.-Aided Mol. Design, 4 (1990) 205.
31. Lewis, R.A. and Dean, P.M., Proc. R. Soc. London, B236 (1989) 125.
32. Singh, J., Saldanha, J. and Thornton, J., Protein Eng., 4 (1991) 251.
33. Moon, J. and Howe, W., Proteins Struct. Funct. Genet., 11 (1991) 314.
34. Rotstein, S. and Murcko, M., J. Comput.-Aided Mol. Design, 7 (1993) 23.
35. Pickett, S.D. and Sternberg, M.J.E., J. Mol. Biol., 231 (1993) 825.
36. Zielinski, P.J., An Annealing Algorithm for Designing Ligands from Receptor Structures, UMI, Ann Arbor, MI, U.S.A., 1994, p. 1.
37. Mayo, S., Olafson, B. and Goddard, W., J. Phys. Chem., 94 (1990) 8897.
38. Cramer, C. and Truhlar, D., J. Am. Chem. Soc., 113 (1991) 8305.
39. Wang, H. and Levinthal, C., J. Comput. Chem., 12 (1991) 868.
40. Cramer, C. and Truhlar, D., J. Am. Chem. Soc., 113 (1991) 8552.
41. Cramer, C. and Truhlar, D., Chem. Phys. Lett., 198 (1992) 74.
42. Cramer, C. and Truhlar, D., J. Comput. Chem., 13 (1992) 1089.
43. Cramer, C. and Truhlar, D., J. Comput.-Aided Mol. Design, 6 (1992) 629.
44. Cramer, C. and Truhlar, D., Science, 256 (1992) 213.
45. Cramer, C. and Truhlar, D., J. Am. Chem. Soc., 114 (1992) 8226.
46. Allen, L., J. Am. Chem. Soc., 111 (1989) 9115.