Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

Journal of Computer-Aided Molecular Design

Volumn 18, Issue 3, 2004, Pages 189-208

  Morley, S David ^a,b   Afshar, Mohammad ^a,c  

^a RiboTargets   (United Kingdom)

^b Enspiral Discovery Limited   (United Kingdom)

^c Ariana Pharma   (France)

Author keywords

Bacterial A site; Cavity detection; Enrichment factor; Guanidine; High throughput docking; HIV 1 TAR; RiboDock ; RNA aptamer; structure based drug design; Virtual screening

Indexed keywords

AUTOMATION; BINDERS; BINDING ENERGY; BINDING SITES; COMPLEXATION; LIGANDS; PROTEINS; RNA;

BACTERIAL A-SITE; CAVITIES DETECTION; ENRICHMENT FACTORS; GUANIDINE; HIGH-THROUGHPUT DOCKING; HIV-1 TAR; RIBODOCK®; RNA APTAMER; STRUCTURE BASED DRUG DESIGNS; VIRTUAL SCREENING;

TAR;

LIGAND; RNA; RNA BINDING PROTEIN;

ARTICLE; AUTOMATION; BINDING SITE; COMPUTER PROGRAM; CONTROLLED STUDY; HUMAN IMMUNODEFICIENCY VIRUS 1; LIGAND BINDING; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RIBOSOME; RNA ANALYSIS; RNA BINDING; SCORING SYSTEM; SCREENING TEST; TRANSACTIVATION;

EID: 4043058000     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:JCAM.0000035199.48747.1e     Document Type: Article

References (42)

1. Shoichet, B.K., McGovern, S.L., Wei, B. and Irwin, J.J., Curr. Opin. Chem. Biol., 6 (2002) 439.
2. Schneider, G. and Böhm, H.-J., Drug Discov. Today, 7 (2002) 64-70.
3. Afshar, M., Prescott, C.D. and Varani, G., Curr. Opin. Biotechnol., 10 (1999) 59.
4. Drysdale, M., Lentzen, G., Matassova, N., Murchie, A., Aboul-Ela, F. and Afshar, M., Prog. Med. Chem., 39 (2002) 73.
5. Carter, A.P., Clemons, W.M., Brodersen, D.E., Morgan-Warren, R.J., Wimberley B.T. and Ramakrish V., Nature, 407 (2000) 340.
6. Brodersen, D.E., Clemons, W.M. Jr., Carter, A.P., Morgan-Warren, R.J., Wimberley B.T. and Ramakrishnan V., Cell, 103 (2000) 1143.
7. Srinivasan, J., Leclerc, F., Xu, W., Ellington, A.D. and Cedergren R., Folding Design, 1 (1996) 463.
8. Leclerc, F. and Cedergren R., J. Med. Chem., 41 (1998) 175.
9. Leclerc, F. and Karplus, M., Theo. Chem. Acc., 101 (1999) 131.
10. Hermann, T. and Westhof, E., J. Med. Chem., 42 (1999) 1250.
11. Filikov, A.V., Mohan, V., Vickers, T.A., Griffey, R.H., Cook, P.D., Abagyan, R.A. and James, T.L, J. Comput.-Aided Mol. Design, 14 (2000) 593.
12. Lind, K.E., Du, Z., Fujinaga, K., Peterlin, B.M. and James, T.L., Chem. Biol., 9 (2002) 185.
13. Ewing, T.J.A. and Kuntz, I.D., J. Comput. Chem., 18 (1997) 1175.
14. Abagyan, R.A., Totrov, M.M. and Kuznetsov, D.N., J. Comput. Chem., 15 (1994) 488.
15. MDL Information Systems, San Leandro, CA.
16. Du, Z., Lind, K.E. and James, T.L., Chem. Biol., 9 (2002) 707.
17. Böhm, H.J., J. Comput.-Aided Mol. Design 8 (1994) 243.
18. Böhm, H.J., J. Comput.-Aided Mol. Design, 12 (1998) 309.
19. Rarey, M, Wefing, S. and Lengauer, T., J. Comput.-Aided Mol. Design, 10 (1996) 41.
20. Schulz-Gasch, T. and Stahl, M., J. Mol. Model. [Online], 9 (2003) 47.
21. Eldridge, M.D., Murray, C.W., Auton, T.R., Paolini, G.V. and Mee, R.P., J. Comput.-Aided Mol. Design, 11 (1997) 425.
22. UK Registered Trade Mark E1308667.
23. Jain, A.N., J. Comput.-Aided Mol. Design, 10 (1996) 427.
24. Yang, Y., Kochoyan, M., Burgstaller, P., Westhof, E. and Famulok, M., Science, 272 (1996) 1343.
25. Hendlich, M., Acta Crystallogr., D54 (1998) 1178.
26. http://relibase.ccdc.cam.ac.uk/
27. We thank reviewer #2 for highlighting the sinA2 correction factor.
28. Wang, Y., Hamasaki, K. and Rando, R.R., Biochemistry, 36 (1997) 768.
29. Murchie, A.I.H., Davis, B., Isel, C., Afshar, M., Drysdale M.J., Bower, J., Potter, A.J., Starkey, I.D., Swarbrick, T.M., Mirza, S., Prescott, C.D., Vaglio, P., Aboul-ela, F. and Karn, J., J. Mol. Biol., 336 (2004) 625.
30. Karn, J. and Prescott, C.D., U.S. Pat. No. 6,573,045 (2003).
31. Davis, B., Afshar, M., Varani, G., Murchie, A.I.H., Karn, J., Lentzen, G., Drysdale, M., Bower, J., Potter, A.J., Starkey I.D., Swarbrick, T.M. and Aboul-ela, F., J. Mol. Biol., 336 (2004) 343.
32. Aboul-ela, F., Karn, J. and Varani G., J. Mol. Biol. 253 (1995) 313.
33. Baurin, N., Baker, R., Richardson, C., Chen, I., Foloppe, N., Potter, A., Jordan, A., Roughley, S., Parratt, M., Greaney, P., Morley, D. and Hubbard, R.E., J. Chem. Inf. Comput. Sci., 44 (2004) 643.
34. Chemical Computing Group, http://www.chemcomp.com/
35. Knowles, D.J.C., Foloppe, N., Matassova, N.B. and Murchie, A.I.H., Curr. Opin. Pharmacol., 2 (2002) 501.
36. Foloppe, N., Chen, I., Davis, B., Hold A., Morley, D. and Howes, R., Bioorg. Med. Chem., 12 (2004) 935.
37. Patel, D.J., Suri, A.K., Jiang, F., Jiang, L., Fan, P., Kumar R.A. and Nonin, S., J. Mol. Biol., 272 (1997) 645.
38. Nissink, J.W.M., Murray, C., Hartshorn, M., Verdonk, M.L., Cole, J.C. and Taylor, R., Proteins, 49 (2002) 457.
39. Kramer, B., Rarey, M. and Lengauer, T., Proteins, 37 (1999) 228.
40. Barril, X., Hubbard, R.E. and Morley, S.D., Mini Reviews in Medicinal Chemistry, accepted.
41. Afshar, M., Caves, L.S., Guimard, L., Hubbard, R.E., Calas, B., Grassy, G. and Haiech, J., J. Mol. Biol., 244 (1994) 554.
42. Hermann, T. and Patel, D.J., Science, 287 (2000) 820.