Combined use of physicochemical data and small-molecule cristallographic contact propensities to predict interactions in protein binding sites

Organic and Biomolecular Chemistry

Volumn 2, Issue 22, 2004, Pages 3238-3249

  Nissink, J Willem M ^a   Taylor, Robin ^a  

^a CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; COMPUTER AIDED ANALYSIS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DATA REDUCTION; KNOWLEDGE ACQUISITION; MOLECULES; SOLVENTS;

CRYSTAL DATA; INTERMOLECULAR CONTACTS; PHYSIOCHEMICAL DATA; PROTEIN DATA BANK (PDB);

PROTEINS;

BULGECIN; DIHYDROFOLATE REDUCTASE; GLYCOPEPTIDE; LIGAND; PROTEIN; SOLVENT;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLOGRAPHY; HYDROPHOBICITY; METABOLISM; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN DATABASE;

BINDING SITES; CHEMISTRY, PHYSICAL; CRYSTALLOGRAPHY; DATABASES, PROTEIN; GLYCOPEPTIDES; HYDROPHOBICITY; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOLVENTS; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 10244257681     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/b405205f     Document Type: Article

References (40)

1. C. C. Blake, D. F. Koenig, G. A. Mair, A. C. North, D. C. Phillips and V. R. Sarma, Nature, 1965, 206, 757-761.
2. C. R. Beddell, P. J. Goodford, F. E. Norrington, S. Wilkinson and R. Wootton, Br. J. Pharmacol., 1976, 57, 201-209.
3. A. Brik and C. H. Wong, Org. Biomol. Chem., 2003, 1, 5-14.
4. G. Klebe, J. Mol. Med., 2000, 78, 269-281.
5. F. C. Bernstein, T. F. Koetzle, G. J. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi and M. Tasumi, J. Mol. Biol., 1977, 112, 535-542.
6. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne, Nucleic Acids Res., 2000, 28, 235-242.
7. F. H. Allen, Acta Crystallogr., Sect. B, 2002, 58, 380-388.
8. M. Tintelnot and P. Andrews, J. Comput. Aided Mol. Des., 1989, 3, 67-84.
9. G. Klebe, J. Mol. Biol., 1994, 237, 212-235.
10. I. J. Bruno, J. C. Cole, J. P. Lommerse, R. S. Rowland, R. Taylor and M. L. Verdonk, J. Comput. Aided Mol. Des., 1997, 11, 525-537.
11. H. J. Bohm, J. Comput. Aided Mol. Des., 1992, 6, 593-606.
12. H. J. Bohm, J. Comput. Aided Mol. Des., 1992, 6, 61-78.
13. D. J. Danziger and P. M. Dean, Proc. R. Soc. London, Ser. B, 1989, 236, 101-113.
14. R. A. Laskowski, J. M. Thornton, C. Humblet and J. Singh, J. Mol. Biol., 1996, 259, 175-201.
15. M. L. Verdonk, J. C. Cole and R. Taylor, J. Mol. Biol., 1999, 289, 1093-1108.
16. M. L. Verdonk, J. C. Cole, P. Watson, V. Gillet and P. Willett, J. Mol. Biol., 2001, 307, 841-859.
17. D. R. Boer, J. Kroon, J. C. Cole, B. Smith and M. L. Verdonk, J. Mol. Biol., 2001, 312, 275-287.
18. J. W. M. Nissink, M. L. Verdonk and G. Klebe, J. Comput. Aided Mol. Des., 2000,14, 787-803.
19. W. R. Pitt and J. M. Goodfellow, Protein Eng., 1991, 4, 531-537.
20. P. Watson, P. Willett, V. J. Gillet and M. L. Verdonk, J. Comput. Aided Mol. Des., 2001, 15, 835-857.
21. P. Labute, Journal of the CCG, 2000, http://www.chemcomp.com.
22. V. V. Rantanen, K. A. Denessiouk, M. Gyllenberg, T. Koski and M. S. Johnson, J. Mol. Biol., 2001, 313, 197-214.
23. H. Gohlke, M. Hendlich and G. Klebe, J. Mol. Biol., 2000, 295, 337-356.
24. G. E. Kellogg, S. F. Semus and D. J. Abraham, J. Comput. Aided Mol. Des., 1991, 5, 545-552.
25. P. J. Goodford, J. Med. Chem., 1985, 28, 849-857.
26. A. Miranker and M. Karplus, Proteins, 1991, 11, 29-34.
27. A. Caflisch, A. Miranker and M. Karplus, J. Med. Chem., 1993, 36, 2142-2167.
28. T. Kortvelyesi, S. Dennis, M. Silberstein, L. Brown, 3rd and S. Vajda, Proteins, 2003, 51, 340-351.
29. M. Silberstein, S. Dennis, L. Brown, T. Kortvelyesi, K. Clodfelter and S. Vajda, J. Mol. Biol., 2003, 332, 1095-1113.
30. D. A. Erlanson, A. C. Braisted, D. R. Raphael, M. Randal, R. M. Stroud, E. M. Gordon and J. A. Wells, Proc Natl Acad Sci USA, 2000, 97, 9367-9372.
31. S. B. Shuker, P. J. Hajduk, R. P. Meadows and S. W. Fesik, Science, 1996, 274, 1531-1534.
32. C. Hansch and A. Leo, Substituent Constants for Correlation Analysis in Chemistry and Biology, John Wiley & Sons, New York, 1979.
33. T. Suzuki and Y. Kudo, J. Comput. Aided Mol. Des., 1990, 4, 155-198.
34. G. Klopman, J.-Y. Li, S. Wang and M. Dimayuga, J. Chem. Inf. Comput. Sci., 1994, 34, 752-781.
35. A. J. Leo, Chem. Rev., 1993, 93, 1281-1306.
36. C. H. Gorbitz and H. P. Hersleth, Acta Crystallogr., Sect. B, 2000, 56 (Pt 3), 526-534.
37. C. H. Gorbitz and H. P. Hersleth, Acta Crystallogr., Sect. B, 2000, 56 (Pt 6), 1094-1102.
38. E. J. van Asselt, K. H. Kalk and B. W. Dijkstra, Biochemistry, 2000, 39, 1924-1934.
39. J. W. M. Nissink, C. Murray, M. Hartshorn, M. L. Verdonk, J. C. Cole and R. Taylor, Proteins, 2002, 49, 457-471.
40. G. Klopman, J.-Y. Li, S. Wang and M. Dimayuga, J. Chem. Inf. Comput. Sci., 1994, 34, 752.