Ligand docking and design in a flexible receptor site

QSAR and Combinatorial Science

Volumn 24, Issue 4, 2005, Pages 503-507

  Alberts, Ian L ^a   Todorov, Nicolay P ^a   Källbku, Per ^a,b   Dean, Philip M ^a  

^a De Novo Pharmaceuticals   (United Kingdom)

^b MEDIVIR AB   (Sweden)

Author keywords

Conformation; Drug design; Flexibility; Protein ligand interaction; Side chain; Structure generation

Indexed keywords

LIGANDS; PROTEINS;

BINDING-SITES; DRUG DESIGN; FLEXIBILITY; LIGAND DESIGN; LIGAND DOCKING; PROTEIN-LIGAND INTERACTIONS; RECEPTOR FLEXIBILITY; RECEPTOR SITES; SIDE-CHAINS; STRUCTURE GENERATION;

BINDING SITES;

CHOLINESTERASE INHIBITOR; COLLAGENASE; DONEPEZIL; HUPERZINE A; INTERSTITIAL COLLAGENASE; LIGAND; RO 31 4724; UNCLASSIFIED DRUG;

BINDING SITE; CONFERENCE PAPER; DRUG DESIGN; METHODOLOGY; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN STRUCTURE; RECEPTOR BINDING; SCORING SYSTEM; SIMULATION;

EID: 20544461834     PISSN: 1611020X     EISSN: None     Source Type: Journal    
DOI: 10.1002/qsar.200430924     Document Type: Conference Paper

References (30)

1. S. J. Teague, Nature Rev. Drug Discov. 2003, 2, 527-540.
2. E. Vieira, A. Binggeli, V. Breu, D. Bur, W. Fischli, R. Guller, G. Hirth, H. P. Marki, M. Muller, C. Oefner, M. Scalone, H. Stadler, M. Wilhelm, W. Wostl, Bioorg. Med. Chem. Lett. 1999, 9, 1397-1402.
3. B. Q. Wei, L. H. Weaver, A. M. Ferrari, B. W. Matthews, B. K. Shoichet, J. Mol. Biol. 2004, 337, 1161-1182.
4. H. Claussen, C. Buning, M. Rarey, T. Lengauer, J. Mol. Biol. 2001, 308, 377-395.
5. C. N. Cavasotto, R. A. Abagyan, J. Mol. Biol. 2004, 337, 209-225.
6. R. M. A. Knegtel, I. D. Kuntz, C. M. Oshiro, J. Mol. Biol. 1997, 266, 424-440.
7. H. B. Broughton, J. Mol. Graph. Model. 2000, 18, 247-257.
8. C. W. Murray, C. A. Baxter, A. D. Frenkel, J. Comput.-Aided Mol. Des. 1999, 13, 547-562.
9. R. Najmanovich, J. Kuttner, V. Sobolev, M. Edelman, Proteins: Struct. Funct. Genet. 2000, 39, 261-268.
10. M. Totrov, R. Abagyan, Proteins: Struct. Funct. Genet. 1997, 29, 215-220.
11. V. Schnecke, L. A. Kuhn, Perpect. Drug Discov. 2000, 20, 171-190.
12. A. R. Leach, J. Mol. Biol. 1994, 235, 345-356.
13. T. M. Frimurer, G. H. Peters, L. F. Iversen, H. S. Andersen, N. P. Moller, O. H. Olsen, Biophys. J. 2003, 84, 2273-2281.
14. A. Caflisch, A. Miranker, M. Karplus, J. Med. Chem. 1993, 36, 2142-2167.
15. H. A. Carlson, Curr. Pharm. Dis. 2002, 8, 1571-1578.
16. M. G. Bursavich, E. H. Rich, J. Med. Chem. 2002, 45, 541-558.
17. H.-J. Böhm, J. Comput.-Aided Mol. Des. 1992, 6, 61-78
18. M. B. Eisen, D. C. Wiley, M. Karplus, R. E. Hubbard, Proteins: Struct. Funct. Genet. 1994, 19, 199-221.
19. V. Gillet, A. P. Johnson, P. Mata, S. Sike, P. Williams, J. Comput.-Aided. Mol. Des. 1994, 7, 127-153.
20. M. Stahl, N. P. Todorov, T. James, H. Mauser, H.-J. Boehm, P. M. Dean, J. Comput.-Aided Mol. Des. 2002, 16, 459-478.
21. G. Kryger, I. Silman, J. L. Sussman, Structure 1999, 7, 297-307.
22. L. M. Coussence, B. Fingleton, L. M. Matrisian, Science 2002, 295, 2387-2392.
23. J. P. Cleutjens, Cardiovasc. Res. 1996, 30, 816-821.
24. B. Lovejoy, A. R. Welsh, S. Carr, C. Luong, C. Broka, R. T. Hendricks, J. A. Campbell, K. A. M. Walker, R. Martin, H. van Wart, M. F. Browner, Nat. Struct. Biol. 1999, 6, 217-221.
25. I. Botos, L. Scapozza, D. Zhang, L. A. Liotta, E. F. Meyer, Proc. Natl. Acad. Sci. USA 1996, 93, 2749-2754.
26. P. Källblad, N. P. Todorov, H. M. G. Willems, I. L. Alberts, J. Med. Chem. 2004, 47, 2761-2767.
27. J. R. Maple, U. Dinur, E. T. Hegler, Proc. Natl. Acad. Sci. USA 1988, 85, 5350-5354.
28. J. A. Erickson, M. Jalaie, D. H. Robertson, R. A. Lewis, M. Vieth, J. Med. Chem. 2004, 47, 45-55.
29. M. L. Raves, M. Harel, Y.-P. Pang, I. Silman, A. P. Kozikowski, J. L. Sussman, Nat. Struct. Biol. 1997, 4, 57-63.
30. N. Borkakoti, F. K. Winkler, D. H. Williams, A. Darcy, M. J. Broadhurst, P. A. Brown, W. H. Johnson, E. J. Murray, Nat. Struct. Biol. 1994, 1, 106-110.