Modelling and simulation: A computational perspective in anticancer drug discovery

Current Medicinal Chemistry - Anti-Cancer Agents

Volumn 4, Issue 5, 2004, Pages 401-403

  Gago, Federico ^a  

^a UNIVERSITY OF ALCALÁ   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT;

BINDING SITE; CANCER CHEMOTHERAPY; CANCER RESEARCH; DRUG DESIGN; DRUG RESEARCH; DRUG STRUCTURE; DRUG TARGETING; HYPOTHESIS; LIGAND BINDING; MACROMOLECULE; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; REVIEW; SIMULATION; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; ANTINEOPLASTIC AGENTS; APOPTOSIS; BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DRUG DESIGN; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SOFTWARE;

EID: 4444281884     PISSN: 15680118     EISSN: None     Source Type: Journal    
DOI: 10.2174/1568011043352786     Document Type: Review

References (54)

1. The Cancer Genome Project, The Wellcome Trust Sanger Institute. http://www.sanger.ac.uk/genetics/CGP/
2. Hurley, L. H.; Boyd, F. L. Trends Pharmacol. Sci., 1988, 9, 402-407.
3. Hurley, L. H. J. Med. Chem., 1989, 32, 2027-2033.
4. Hurley, L. H. Nat. Rev. Cancer, 2002, 2, 188-200.
5. Noble, D.; Levin, J.; Scott, W. Drug Discov. Today, 1999, 4, 10-16.
6. Bader, G. D.; Betel, D.; Hogue, C. W. Nucleic Acids Res., 2003, 31, 248-250 (http://www.blueprint.org/bind/bind.php).
7. Babul, M. M.; Luscombe, N. M.; Aravind, L.; Gerstein, M.; Teichmann, S. A. Curr. Opin. Struct. Biol., 2004, 14, 283-291.
8. Reddy, A.; Kaelin, W. G. Curr. Opin. Pharmacol., 2002, 2, 366-373.
9. Scherf, U.; Ross, D. T.; Waltham, M.; Smith, L. H.; Lee, J. K.; Tanabe, L.; Kohn, K. W.; Reinhold, W. C.; Myers, T. G.; Andrews, D. T.; Scudiero, D. A.; Eisen, M. B.; Sausville, E. A.; Pommier, Y.; Botstein, D.; Brown, P. O.; Weinstein, J. N. Nat. Genet., 2000, 24, 236-244.
10. Hughes, T. R.; Marton, M. J.; Jones, A. R.; Roberts, C. J.; Stoughton, R.; Armour, C. D.; Bennett, H. A.; Coffey, E.; Dai, H.; He, Y. D.; Kidd, M. J.; King, A. M.; Meyer, M. R.; Slade, D.; Lum, P. Y.; Stepaniants, S. B.; Shoemaker, D. D.; Gachotte, D.; Chakraburtty, K.; Simon, J.; Bard, M.; Friend, S. H. Cell, 2000, 102, 109-126.
11. Zambrowicz, B. P.; Sands, A. T. Nat. Rev. Drug Discov., 2003, 2, 38-51.
12. Zambrowicz, B. P.; Turner, C. A.; Sands, A. T. Curr. Opin. Pharmacol., 2003, 3, 1-8.
13. http://www.umass.edu/microbio/rasmol/
14. http://www.expasy.org/spdbv/
15. http://www.accelrys.com/viewer/
16. http://www.ks.uiuc.edu/Research/vmd/
17. http://www.mdlchime.com/chime/
18. Kazlauskas R. Science, 2001, 293, 2277-2279.
19. van Dongen, M.; Weigelt, J.; Uppenberg, J.; Schultz, J.; Wikström, M. Drug Discov. Today, 2002, 7, 471-478.
20. Coles, M.; Heller, M.; Kessler, H. Drug Discov. Today, 2003, 8, 803-810.
21. Sali, A.; Kuriyan, J. Trends Cell Biol., 1999, 9, M20-M24.
22. Marti-Renom, M. A., Stuart, A. C.; Fiser, A.; Sánchez, R.; Melo, F.; Sali, A. Ann. Rev. Biophys., 2000, 29, 291-325.
23. Campbell, S. J.; Gold, N. D.; Jackson, R. M.; Westheady, D. R. Curr. Opin. Struct. Biol., 2003, 13, 389-395.
24. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J. Comput. Aid. Mol. Des., 2002, 16, 151-166.
25. Glen, R. C.; Allen, S. C. Curr. Med. Chem., 2003, 10, 763-777.
26. Smith, G. R.; Sternberg, M. J. E. Curr. Opin. Struct. Biol., 2002, 12, 28-35.
27. Wodak, S. J.; Méndez, R. Curr. Opin. Struct. Biol., 2004, 14, 242-249.
28. Karplus, M. Acc. Chem. Res., 2002, 35, 321-322.
29. Cheatham, T. E., III; Cieplak, P.; Kollman, P. A. J. Biomol. Struct. Dyn., 1999, 16, 845-862.
30. MacKerell, A. D., Jr.; Banavali, N. K. J. Compul. Chem., 2000, 21, 105-120.
31. Cheatham, T. E.; Kollman, P. A. Annu. Rev. Phys. Chem., 2000, 51, 435-471.
32. Sagui, C.; Darden, T. A. Annu. Rev. Biophys. Biomol. Struct., 1999, 28, 155-179.
33. Giudice, E.; Lavery, R. Acc. Chem. Res., 2002, 35, 350-357.
34. Cheatham, T. E. Curr. Opin. Struct. Biol., 2004, 14, 360-367.
35. Duan, Y.; Kollman, P. A. Science, 1998, 282, 740-744.
36. Bashford, D.; Case, D. Annu. Rev. Phys. Chem., 2000, 51, 129-152.
37. Young, M. A.; Gonfloni, S.; Superti-Furga, G.; Roux, B.; Kurigan, J. Cell, 2001, 105, 115-126.
38. Mendieta, J.; Martín-Santamaría, S.; Priego, E.-M.; Balzarini, J.; Camarasa, M.-J.; Pérez-Pérez, M.-J.; Gago, F. Biochemistry, 2004, 43, 405-414.
39. Isralewitz, B.; Gao, M.; Schulten, K. Curr. Opin. Struct. Biol., 2001, 11, 224-230.
40. Ma, J.; Karplus, M. Proc. Natl. Acad. Sci. USA, 1997, 94, 11905-11910.
41. Marco, E. ; García-Nieto, R.; Gago, F. J. Mol. Biol., 2003, 328, 9-32.
42. Zaman, G. J. R.; Michiels, P. J.; van Boeckel, C. A. Drug Discov. Today, 2003, 8, 297-306.
43. Hunter, T. Cell, 2000, 100, 113-127.
44. Hubbard, S. R. Curr. Opin. Struct. Biol., 2002, 12, 735-741.
45. Klumpp, S.; Krieglstein, J. Curr. Opin. Pharmacol., 2002, 2, 458-462.
46. McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature, 1977, 267, 585-590.
47. Chien, A.; Foster, I.; Goddette, D. Drug Discov. Today, 2002, 15, S176-S180.
48. Foldingηomeproject: http://www.stanford.edu/group/pandegroup/folding/
49. http://www.chem.ox.ac.uk
50. http://www.chem.ox.ac.uk/ccdd/ccdd.html
51. Davies, E.K.; Glick, M.; Harrison, K.N.; Richards, W.G. J Comput. Chem., 2002, 23, 1544-1550.
52. Eldridge, M.D.; Murray, C.W.; Auton, T.R.; Paolini, G.V; Mee, R.P. J. Comput.-Aided Mol. Des., 1997, 11, 425-445.
53. Davies, E. K.; Richards, W. G. Drug Discov. Today, 2002, 7, S99-S103.
54. Lazo, J.S.; Ducruet, A.P.; Koldamova, R. P. Mol. Pharmacol., 2003, 64, 199-201.