Architectural repertoire of ligand-binding pockets on protein surfaces

ChemBioChem

Volumn 11, Issue 4, 2010, Pages 556-563

  Weisel, Martin ^a   Kriegl, Jan M ^b   Schneider, Gisbert ^a,c  

^a GOETHE UNIVERSITY   (Germany)

^b BOEHRINGER INGELHEIM PHARMA GMBH AND CO KG   (Germany)

^c ETH ZURICH   (Switzerland)

Author keywords

Bioinformatics; Drug design; Neural networks; Pocketome; Protein folding

Indexed keywords

ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTOMATION; BINDING AFFINITY; BINDING SITE; COMPUTER PROGRAM; LIGAND BINDING; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; RECEPTOR AFFINITY; STRUCTURE ANALYSIS;

BINDING SITES; DATABASES, PROTEIN; HSP90 HEAT-SHOCK PROTEINS; LIGANDS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 77149174813     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200900604     Document Type: Article

References (53)

1. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliliand, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucleic Acids Res. 2000, 28, 235-242.
2. J. W. M. Nissink, C. Murray, M. Hartshorn, M. L. Verdonk, J. C. Cole, R. Taylor, Proteins 2002, 49, 457-471.
3. G. Klebe, J. Mol. Med. 2000, 78, 269-281.
4. P. J. Gane, P. M. Dean, Curr. Opin. Struct. Biol. 2000, 10, 401-404.
5. C. A. Orengo, T. P. Flores, D. T. Jones, W. R. Taylor, J. M. Thornton, Curr. Biol. 1993, 3, 131-139.
6. M. Gerstein, H. Hegyi, FEMS Microbiol. Rev. 1998, 22, 277-304.
7. M. Wang, L. S. Yafremava, D. Caetano-Anollés, J. E. Mittenthal, G. Caetano-Anollés, Genome Res. 2007, 17, 1572-1585.
8. E. V. Koonin, Y. I. Wolf, G. P. Karev, Nature 2002, 420, 218-223.
9. A. Harrison, F. Pearl, R. Mott, J. M. Thornton, C. A. Orengo, J. Mol. Biol. 2002, 323, 909-926.
10. C. A. Orengo, A. D. Michie, D. T. Jones, M. B. Swindells, J. M. Thornton, Structure 1997, 5, 1093-1108.
11. A. L. Cuff, L. Silitoe, T. Lewis, O. C. Redfern, R. Garatt, J. M. Thornton, C. A. Orengo, Nucl. Acids Res. 2009, 37, D310-D314.
12. G. Apic, J. Gough, S. A. Teichmann, J. Mol. Biol. 2001, 310, 311-325.
13. C. Chothia, J. Gough, C. Vogel, S. A. Teichmann, Science 2003, 300, 1701-1703.
14. A. C. R. Martin, C. A. Orengo, E. G. Hutchinson, S. Jones, M. Karmiranztou, R. A. Laskowski, J. B. O. Mitchell, C. Taroni, J. M. Thornton, Structure 1998, 6, 875-884.
15. J. M. Thornton, A. E. Todd, D. Milburn, N. Borkakoti, C. A. Orengo, Nat. Struct. Biol. 2000, 7, 991-994.
16. C. A. Orengo, J. M. Thornton, Annu. Rev. Biochem. 2005, 74, 867-900.
17. S. Schmitt, D. Kuhn, G. Klebe, J. Mol. Biol. 2002, 323, 387-406.
18. M. Weisel, E. Proschak, G. Schneider, Chem. Cent. J. 2007, 1, 7.
19. R. A. Laskowski, J. Mol. Graph. 1995, 13, 323-330.
20. J. Liang, H. Edelsbrunner, C. Woodward, Protein Sci. 1998, 7, 1884-1897.
21. T. Binkowski, S. Naghibzadeh, J. Liang, Nucleic Acids Res. 2003, 31, 3352-3355.
22. B. Fritzke, Neural Networks 1994, 7, 1441-1460.
23. B. Fritzke in: Advances in Neural Information Processing Systems (Eds.: G. Tesauro, D. S. Touretzky, T. K. Leen), MIT Press, Cambridge, 1995, pp. 625-632.
24. K. Lindorff-Larsen, P. Røgen, E. Paci, M. Vendruscolo, C. M. Dobson, Trends Biochem. Sci. 2005, 30, 13-19.
25. G. P. Brady, Jr., P. F. W. Stouten, J. Comput. Aided Mol. Des. 2000, 14, 383-401.
26. M. Hendlich, F. Rippmann, G. Barnickel, J. Mol. Graphics Model. 1997, 15, 359-363.
27. B. Huang, M. Schrçder, BMC Struct. Biol. 2006, 6, 19-29.
28. M. Weisel, E. Proschak, J. M. Kriegl, G. Schneider, Proteomics 2009, 9, 451-459.
29. B. Stauch, H. Hofmann, M. Perkovic, M. Weisel, F. Kopietz, K. Cichutek, C. Münk, G. Schneider, Proc. Natl. Acad. Sci. USA 2009, 106, 12079-12084.
30. T. Kohonen, Self-Organization and Associative Memory, Springer, Berlin, 1989.
31. T. M. Martinetz, K. J. Schulten in: Artificial Neural Networks (Eds.: T. Kohonen, K. Mäkisara, O. Simula, J. Kangas), North-Holland, Amsterdam, 1991, pp. 397-402.
32. B. T. Fan, A. Panaye, J. P. Doucet, A. Barbu, J. Chem. Inf. Comput. Sci. 1993, 33, 657-662.
33. R. Balducci, R. S. Pearlman, J. Chem. Inf. Comput. Sci. 1994, 34, 822-831.
34. R. Wang, X. Fang, Y. Lu, S. Wang, J. Med. Chem. 2004, 47, 2977-2980.
35. R. Wang, X. Fang, Y. Lu, C.-Y. Yang, S. Wang, J. Med. Chem. 2005, 48, 4111-4119.
36. A. Dalby, J. G. Nourse, W. D. Hounshell, A. K. I. Gushurst, D. L. Grier, B. A. Leland, J. Laufer, J. Chem. Inf. Comput. Sci. 1992, 32, 244-255.
37. P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. Wang, D. Ramage, N. Amin, B. Schwikowski, T. Ideker, Genome Res. 2003, 13, 2498-2504.
38. P. Willett, J. Med. Chem. 2005, 48, 4183-4199.
39. Daylight Theory Manual: http://www.daylight.com/dayhtml/doc/theory/index. html (version May, 2009).
40. S. Ash, M. A. Cline, R. W. Homer, T. Hurst, G. B. Smith, J. Chem. Inf. Comput. Sci. 1997, 37, 71-79.
41. E. Proschak, J. K. Wegner, A. Schüller, G. Schneider, U. Fechner, J. Chem. Inf. Model. 2007, 47, 295-301.
42. A. K. Ghose, G. M. Crippen, J. Comput. Chem. 1986, 7, 565-577.
43. V. N. Viswanadhan, A. K. Ghose, G. R. Revankar, R. K. Robins, J. Chem. Inf. Comput. Sci. 1989, 29, 163-172.
44. G. Moreau, P. Broto, Nouv. J. Chim. 1980, 4, 757-764.
45. P. Broto, G. Moreau, C. Vandyke, Eur. J. Med. Chem. 1984, 19, 66-70.
46. H. Bauknecht, A. Zell, H. Bayer, P. Levi, M. Wagener, J. Sadowski, J. Gasteiger, J. Chem. Inf. Comput. Sci. 1996, 36, 1205-1213.
47. G. Schneider, W. Neidhart, T. Giller, G. Schmid, Angew. Chem. 1999, 111, 3068-3070;
48. Angew. Chem. Int. Ed. 1999, 38, 2894-2896.
49. U. Fechner, L. Franke, S. Renner, P. Schneider, G. Schneider, J. Comp. Aided Mol. Des. 2003, 17, 687-698.
50. S. Renner, G. Schneider, J. Med. Chem. 2004, 47, 4653-4664.
51. Y. Tanrikulu, M. Nietert, U. Scheffer, E. Proschak, K. Grabowski, P. Schneider, M. Weidlich, M. Karas, M. Gçbel, G. Schneider, ChemBioChem 2007, 8, 1932-1936.
52. A. Klenner, M. Weisel, F. Reisen, E. Proschak, G. Schneider, Mol. Inf. 2010, in press.
53. A. Kahraman, R. J. Morris, R. A. Laskowski, J. M. Thornton, J. Mol. Biol. 2007, 368, 283-301.