Scoring functions: A view from the bench

Journal of Computer-Aided Molecular Design

Volumn 13, Issue 2, 1999, Pages 99-108

  Tame, Jeremy R H ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Binding; Ligand; Protein; Thermodynamics

Indexed keywords

BINDING ENERGY; LIGANDS; PHYSICAL CHEMISTRY; THERMODYNAMICS;

BINDING; COMPUTATIONAL APPROACH; DRUG DESIGN; MOLECULE LIGANDS; NON-COVALENT INTERACTION; POTENTIAL LIGAND; PROTEIN TARGETS; SCORING FUNCTIONS; SMALL MOLECULES; TARGET MOLECULE;

PROTEINS;

DRUG BINDING; DRUG DESIGN; LIGAND BINDING; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; REVIEW; THERMODYNAMICS;

EID: 0032993815     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008068903544     Document Type: Review

References (62)

1. Verlinde, C.L.M.J. and Hol, W.G.J., Structure, 2 (1994) 577.
2. Böhm, H.-J., Prog. Biophys. Mol. Biol., 66 (1996) 197.
3. Janin, J., Proteins, 21 (1995) 30.
4. Knegtel, R.M.A. and Grootenhuis, P.D.J., Perspect. Drug Discov. Des., 9/10/11 (1998) 99.
5. Kollman, P., Chem. Rev., 93 (1993) 2395.
6. Ajay and Murcko, M.A., J. Med. Chem., 38 (1996) 4953.
7. Gilson, M.K., Given, J.A., Bush, B.L. and McCammon, J.A., Biophys. J., 72 (1997) 1047.
8. Hubbard, R.E., Curr. Opin. Struct. Biotechnol., 8 (1997) 696.
9. Miyamoto, S. and Kollman, P., Proteins, 16 (1993) 226.
10. Cieplak, P. and Kollman, P.A., J. Comput.-Aided Mol. Design, 7 (1993) 291.
11. Gustchina, A., Samson, C., Prevost, M., Richelle, J., Wodak, S.Y., Wlodawer, A. and Weber, I.T., Protein Eng., 7 (1994) 309.
12. Eisenberg, D. and Maclachlan, A.D., Nature, 319 (1986) 199.
13. Böhm, H.-J., J. Comput.-Aided Mol. Design, 8 (1994) 243.
14. Wallace, R.B., Johnson, M.J., Hirose, T., Miyake, T., Kawashima, E.H. and Itakura, K., Nucleic Acids Res., 9 (1981) 879.
15. Clackson, T. and Wells, J.A., Science, 267 (1995) 383.
16. Jencks, W.P., Proc. Natl. Acad. Sci. USA, 78 (1981) 4046.
17. Perutz, M.F., Shih, D.T.B. and Williamson, D., J. Mol. Biol., 239 (1994) 555.
18. Colombo, M.F., Rau, D.C. and Parsegian, V.A., Science, 256 (1992) 655.
19. Page, M. and Jencks, W.P., Proc. Natl. Acad. Sci. USA, 68 (1971) 1678.
20. Doig, A.J. and Sternberg, M.J.E., Protein Sci., 4 (1995) 2247.
21. Erickson, H.P., J. Mol. Biol., 206 (1989) 465.
22. Sturtevant, J.M., Proc. Natl. Acad. Sci. USA, 74 (1977) 2236.
23. Tame, J.R.H., Sleigh, S.H., Wilkinson, A.J. and Ladbury, J.E., Nat. Struct. Biol., 3 (1996) 998.
24. Sippl, M.J., Ortner, M., Jaritz, M., Lackner, P. and Flockner, H., Folding Des., 1 (1996) 289.
25. Verkhiver, G., Appelt, K., Freer, S.T. and Villafranca, J.E., Protein Eng., 8 (1995) 677.
26. Wallquist, A., Jernigan, R.L. and Covell, D.G., Protein Sci., 4 (1995) 1881.
27. Zhang, C., Vasmatzis, G., Cornette, J.L. and Delisi, C., J. Mol. Biol., 267 (1997) 707.
28. BenNaim, A., J. Chem. Phys., 107 (1997) 3698.
29. Xu, D., Lin, S.L. and Nussinov, R., J. Mol. Biol., 265 (1997) 68.
30. Horton, N. and Lewis, M., Protein Sci., 1 (1992) 169.
31. Chothia, C., Nature, 248 (1974) 338.
32. Fersht. A.R., Trends Biochem. Sci., 12 (1987) 301.
33. Vallone, B., Miele, A.E., Vecchini, P., Chiancone, E. and Brunori, M., Proc. Natl. Acad. Sci. USA, 95 (1998) 6103.
34. Honig, B. and Nicholls, A., Science, 268 (1995) 1144.
35. Warshel, A. and Papazyan, A., Curr. Opin. Struct. Biol., 8 (1998) 211.
36. Privalov, P.L. and Gill, S.J., Adv. Protein Chem., 40 (1988) 191.
37. Muller, N., Acc. Chem. Res., 23 (1990) 23.
38. Laidig, K.E. and Daggett, V., J. Phys. Chem., 100 (1996) 5616.
39. Williams, D.H., Cox, J.P.L., Doig, A.J., Gardner, M., Gerhard, U., Kaye, P.T., Lal, A.R., Nicholls, I.A., Salter, C.J. and Mitchell, R.G., J. Am. Chem. Soc., 113 (1991) 7020.
40. Searle, M.S., Williams, D.H. and Gerhard, U., J. Am. Chem. Soc., 114 (1992) 10697.
41. Juffer, A.H., Eisenhaber, F., Hubbard, S.J., Walter, D. and Argos, P., Protein Sci., 4 (1995) 2499.
42. Weber, G., Protein Interactions, Chapman and Hall, New York, NY, 1992.
43. Hensley, P., Structure, 4 (1996) 367.
44. Ladbury, J.E. and Chowdhry, B.Z., Chem. Biol., 3 (1996) 791.
45. Brandts, J.F. and Lin, L.N., Biochemistry, 29 (1990) 6927.
46. Garland, P.B., Quart. Rev. Biophys., 29 (1997) 91.
47. Schuck, P. and Minton, A.P., Trends Biochem. Sci., 21 (1996) 458.
48. Dunitz, J.D., Chem. Biol., 2 (1995) 709.
49. Franks, F., Water, Royal Society of Chemistry, London, 1984.
50. Dunitz, J.D., Science, 264 (1994) 670.
51. Bhat, T.N. Bertley, G.A., Boulot, G., Greene, M.I., Tello, D., Dallacqua, W., Souchon, H., Schwarz, F.P., Mariuzza, R.A. and Poljak, R.J., Proc. Natl. Acad. Sci. USA, 91 (1994) 1089.
52. Tame, J.R.H., Murshudov, G.N., Dodson, E.J., Neil, T.K., Dodson, G.G., Higgins, C.F. and Wilkinson, A.J., Science, 264 (1994) 1578.
53. Pearlman, D.A. and Connelly, P.R., J. Molo. Biol., 248 (1995) 696.
54. Poornima, C.S. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 513.
55. Ladbury, J.E., Chem. Biol., 3 (1996) 973.
56. Mikol, V., Papageorgiou, C. and Borer, X., J. Med. Chem., 38 (1995) 3361.
57. Jain, A.N., J. Comput.-Aided Mol. Design, 10 (1996) 427.
58. Searle, M.S. and Williams, D.H., J. Am. Chem. Soc., 114 (1992) 10690.
59. Oprea, T.I. and Marshall, G.R., Perspect. Drug Discov. Des., 9/10/11 (1998) 35.
60. Krystek, S., Stouch, T. and Novotny, J., J. Mol. Biol., 234 (1993) 661.
61. Gilson, M.K., Given, J.A. and Head, M.S., Chem. Biol., 4 (1997) 87.
62. Zimmerman, S.C. and Murray, T.J., Phil. Trans. R. Soc. London, A 345 (1993) 49.