Docking of small ligands to low-resolution and theoretically predicted receptor structures

Journal of Computational Chemistry

Volumn 23, Issue 1, 2002, Pages 189-197

  Wojciechowski, Marek ^a   Skolnick, Jeffrey ^a  

^a DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

Author keywords

Cocrystallized complexes; Induced fit; Ligand docking; Low resolution protein models; Protein structure prediction

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; CARRIER PROTEIN; CELL SURFACE RECEPTOR; ESCHERICHIA COLI PROTEIN; LIGAND; MALTODEXTRIN BINDING PROTEIN, E COLI; MALTODEXTRIN-BINDING PROTEIN, E COLI;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; FACTUAL DATABASE; MACROMOLECULE; PROTEIN CONFORMATION;

ALGORITHMS; AMINO ACIDS; BACTERIAL PROTEINS; BINDING SITES; CARRIER PROTEINS; DATABASES, FACTUAL; ESCHERICHIA COLI PROTEINS; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; RECEPTORS, CELL SURFACE;

EID: 0037079587     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.1165     Document Type: Article

References (36)

1. 1 Pillardy, J. ; Czaplewski, C. ; Liwo, A. ; Lee, J. ; Ripoll, D. R. ; Kazmierkiewicz, R. ; et al. Proc Natl Acad Sci USA 2001, 98, 2329.
2. 2 Marchler‐Bauer, A. ; Bryant, S. H. Proteins 1999, 37, 218.
3. 3 Gschwend, D. A. ; Good, A. C. ; Kuntz, I. D. J Mol Recognit 1996, 9, 175.
4. 4 Read, R. J. ; Hart, T. N. ; Cummings, M. D. Ness, S. R. Supramol Chem 1995, 6, 135.
5. 5 Leach, A. R. J Mol Biol 1994, 235, 345.
6. 6 Blaney, J. M. ; Dixon, J. S. Perspect Drug Dis Design 1993, 1, 301.
7. 7 Katchalski‐Katzir, E. ; Shariv, I. ; Eisenstein, M. ; Friesem, A. A. ; Aflalo, C. ; Vakser, I. A. Proc Natl Acad Sci USA 1992, 89, 2195.
8. 8 Gabb, H. A. ; Jackson, R. M. ; Sternberg, M. J. E. J Mol Biol 1997, 272, 106.
9. 9 Kuntz, I. D. ; Blaney, J. M. ; Oatley, S. J. ; Langridge, R. ; Ferrin, T. A. J Mol Biol 1982, 161, 269.
10. 10 Jiang, F. ; Kim, S. H. J Mol Biol 1991, 219, 79.
11. 11 Desmet, J. ; Wilson, I. A. ; Joniau, M. ; DeMaeyer, M. ; Lasters, I. FASEB J 1997, 11, 164.
12. 12 Morris, G. M. ; Goodsell, D. S. ; Huey, R. ; Olson, A. J. J Comput Aid‐Mol Design 1996, 10, 293.
13. 13 Peters, K. P. ; Fauck, J. ; Frommel, C. J Mol Biol 1996, 256, 201.
14. 14 Laskowski, R. A. ; Luscombe, N. M. ; Swindells, M. B. ; Thornton, J. M. Protein Sci 1996, 5, 2438.
15. 15 Weng, Z. P. ; Vajda, S. ; Delisi, C. Protein Sci 1996, 5, 614.
16. 16 Robert, C. H. ; Janin, J. J Mol Biol 1998, 283, 1037.
17. 17 Muegge, I. ; Martin, Y. C. J Med Chem 1999, 42, 791.
18. 18 Norel, R. ; Lin, S. L. ; Wolfson, H. J. ; Nussinov, R. J Mol Biol 1995, 252, 263.
19. 19 Norel, R. ; Petrey, D. ; Wolfson, H. J. ; Nussinov, R. Protein Struct Funct Genet 1999, 36, 307.
20. 20 Palma, P. N. ; Krippahl, L. ; Wampler, J. E. ; Moura, J. J. G. Protein Struct Funct Genet 2000, 39, 372.
21. 21 Vakser, I. A. Protein Eng 1996, 9, 37.
22. 22 Vakser, I. A. Biopolymers 1996, 39, 455.
23. 23 Vakser, I. A. ; Matar, O. G. ; Lam, C. F. Proc Natl Acad Sci USA 1999, 96, 8477.
24. 24 Vakser, I. A. Protein Struct Funct Genet 1997, 1, 226.
25. 25 Vakser, I. A. Protein Eng 1995, 8, 371.
26. 26 Ritchie, D. W. ; Kemp, G. J. L. Protein Struct Funct Genet 2000, 39, 178.
27. 27 Trosset, J. Y. ; Scheraga, H. A. Proc Natl Acad Sci USA 1998, 95, 8011.
28. 28 Skolnick, J. ; Kihara, D. Proteins 2001, 42, 319.
29. 29 Kolinski, A. ; Rotkiewicz, P. ; Ilkowski, B. ; Skolnick, J. Proteins 1999, 37, 592.
30. 30 Bernstein, F. C. ; Koetzle, T. F. ; Williams, G. J. B. ; Meyer, E. F., Jr. ; Brice, M. D. ; Rodgers, J. R. ; et al. J Mol Biol 1977, 112, 535.
31. 31 Sharff, A. J. ; Rodseth, L. E. ; Spurlino, J. C. ; Quiocho, F. A. Biochemistry 1992, 31, 10657.
32. 32 Schulz, G. E. Faraday Discuss 1992, 93, 85.
33. 33 Fischer, D. ; Elofsson, A. ; Rice, D. ; Eisenberg, D. Pac Symp Biocomput 1996, 300.
34. 34 http://www.doe‐mbi.ucla.edu/people/fischer/BENCH/table1.html. UCLA. 1996, Abstract.
35. 35 Benning, M. M. ; Smee, A. F. ; Wells, M. A. ; Holden, H. M. J Mol Biol 1992, 228, 208.
36. 36 Meyer, M. ; Wilson, P. ; Schomburg, D. J Mol Biol 1996, 264, 199.