Computational resources for protein modelling and drug discovery applications

Infectious Disorders - Drug Targets

Volumn 9, Issue 5, 2009, Pages 557-562

  Dhaliwal, B ^a   Chen, Yu Wai ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Homology modelling; Molecular docking; Structure based drug design; Virtual screening

Indexed keywords

BINDING SITE; COMPUTER GRAPHICS; COMPUTER MODEL; COMPUTER PROGRAM; DRUG DESIGN; DRUG TARGETING; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR LIBRARY; MOLECULAR MODEL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; VALIDATION PROCESS; WEB BROWSER;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DESIGN; DRUG DISCOVERY; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 70349542581     PISSN: 18715265     EISSN: None     Source Type: Journal    
DOI: 10.2174/187152609789105669     Document Type: Review

References (47)

1. Buchanan S.G. Curr. Opin. Drug. Discov. Dev., 2002, 5, 367-381.
2. Blundell, T.; Carney, D.; Gardner, S.; Hayes, F.; Howlin, B.; Hubbard, T.; Overington, J.; Singh, D.A.; Sibanda, B.L.; Sutcliffe, M. Eur. J. Biochem., 1988, 172, 513-520.
3. Koppe, J.; Scwede, T. Pharmacogenomics, 2004, 5, 405-416.
4. Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. J. Mol. Biol., 1963, 7, 95-99.
5. Evans, P.R. Acta Crystallogr., 2007, D63, 58-61.
6. Sperandio, O.; Miteva, M.A.; Delfaud, F.; Villoutreix, B.O. Curr. Protein Pept. Sci., 2006, 7, 369-393.
7. Jain, A.N. Curr. Opin. Drug. Discov. Dev., 2004, 7, 396-403.
8. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. Nucleic Acids Res., 2000, 28, 235-242.
9. Laskowski, R.A. Nucleic Acids Res., 2009, 37, 355-359.
10. Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R.D.; Bairoch, A. Nucleic Acids Res., 2003, 31, 3784-3788.
11. Notredame, C.; Higgins, D.G.; Heringa, J. J. Mol. Biol., 2000, 302, 205-217.
12. Larkin, M.A.; Blackshields,G.; Brown, G.P.; Chenna, R.; McGettigan, P.A.; McWilliam, H.; Valentin, F.; Wallace, I.M.; Wilm, A.; Lopez R.; Thompson, J.D.; Gibson, T.J.; Higgins, D.G. Bioinformatics, 2007, 23, 2947-2948.
13. Edgar, R.C. Nucleic Acids Res., 2004, 32, 1792-1797.
14. Holm, L.; Kääriäinen, S.; Rosenström, P.; Schenkel, A. Bioinformatics, 2008, 24, 2780-2781.
15. Jones, D.T. J. Mol. Biol., 1999, 292, 195-202.
16. Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. Bioinformatics, 2006, 22, 195-201.
17. Lambert, C.; Léonard, N.; De Bolle, X.; Depiereux, E. Bioinformatics, 2002, 18, 1250-1256.
18. Fiser, A.; Sali, A. Methods Enzymol., 2003, 374, 463-491.
19. Collaborative Computational Project, Number 4. Acta Crystallogr., 1994, D50, 760-763.
20. Adams, P.D.; Grosse-Kunstleve, R.W.; Hung, L.W.; Ioerger, T.R.; McCoy, A.J.; Moriarty, N.W.; Read, R.J.; Sacchettini, J.C.; Sauter, N.K.; Terwilliger, T.C. Acta Crystallogr., 2002, D58, 1984-1954.
21. Davis, I.W.; Leaver-Fay, A.; Chen, V.B.; Block, J.N.; Kapral, G.J.; Wang, X.; Murray, L.W.; Arendall, W.B. 3rd; Snoeyink, J.; Richardson, J.S.; Richardson, D.C. Nucleic Acids Res., 2007, 35, 375-383.
22. Walters, P.; Stahl, M. University of Arizona, 1994.
23. Kleywegt, G.J.; Jones T.A. Acta Crystallogr., 1994, D50, 178-185.
24. Kleywegt, G.J.; Jones, T.A. Acta Crystallogr., 1999, D55, 941-944.
25. Huang, B.; Schroeder, M. BMC Struct. Biol., 2006, 6, 19.
26. Landau, M.; Mayrose, I.; Rosenberg, Y.; Glaser, F.; Martz, E.; Pupko, T.; Ben-Tal, N. Nucleic Acids Res., 2005, 33, 299-302.
27. Ritchie, D.W.; Kozakov, D.; Vajda, S. Bioinformatics, 2008, 24, 1865-1873.
28. Comeau, S.R.; Kozakov, D.; Brenke, R.; Shen, Y.; Beglov, D.; Vajda, S. Proteins, 2007, 69, 781-785.
29. Morris, G.M.; Huey, R.; Olson, A.J. Curr. Protoc. Bioinformatics, 2008, Chapter 8, Unit 8.14.
30. Schuettelkopf, A.W.; van Aalten, D.M. Acta Crystallogr., 2004, D60, 1355-1363.
31. Wishart,D.S.; Knox, C.; Guo, A.C.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey J. Nucleic Acids Res., 2006, 34, 668-672.
32. Chang, A.; Scheer, M.; Grote, A.; Schomburg, I.; Schomburg, D. Nucleic Acids Res., 2009, 37, 588-592.
33. Irwin, J.J.; Shoichet, B.K. J. Chem. Inf. Model., 2005, 45, 177-182.
34. Chen, J.; Swamidass, S.J.; Dou, Y.; Bruand, J.; Baldi, P. Bioinformatics, 2005, 21, 4133-4139.
35. Degtyarenko, K.; Matos, P. de; Ennis, M.; Hastings, J.; Zbinden,M.; McNaught, A.; Alcántara, R.; Darsow, M.; Guedj, M.; Ashburner, M. Nucleic Acids Res., 2008, 36, 344-350.
36. Wang, Y.; Xiao, J.; Chen, V.B.; Suzek, T.O.; Zhang, J.; Wang, J.; Bryant, S.H. Nucleic Acids Res., 2009, 37, W623-W633.
37. Hur, J.; Wild, D.J. Chem. Cent. J., 2008, 2, 11.
38. Emsley, P.; Cowtan, K. Acta Crystallogr., 2004, D60, 2126-2132.
39. DeLano, W. The PyMOL Mol. Graph. Syst., 2002.
40. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph., 1996, 14, 33-38.
41. Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M.C. Nucleic Acids Res., 2003, 31, 3381-3385.
42. Bonneau, R; Strauss, C.E.; Rohl, C.A.; Chivian, D.; Bradley, P.; Malmstrom, L.; Robertson,T.; Baker, D. J. Mol. Biol., 2002, 322, 65-78.
43. Rohl,C.A.; Strauss, C.E.; Chivian, D.; Baker, D. Proteins, 2004, 55, 656-77.
44. Misura, K.M.S.; Chivian, D.; Rohl, C.A.; Kim, D.E.; Baker, D. Proc. Natl. Acad. Aci. USA, 2006, 103, 5361-5366.
45. Cross, S.S. J. Chem. Inf. Model., 2005, 45, 993-1001.
46. Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R. J. Mol. Biol., 1997, 267, 727-748.
47. Wolber, G.; Langer, T. J. Chem. Inf. Model., 2005, 45, 160-169.