A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers

Journal of Computer-Aided Molecular Design

Volumn 22, Issue 9, 2008, Pages 681-691

  Dorfman, Roman J ^a   Smith, Karl M ^a   Masek, Brian B ^a   Clark, Robert D ^a  

^a Tripos Informatics Research Center   (United States)

Author keywords

Bioactive conformation; Conformational sampling; Conformer generation; Docking; Pharmacophores; Shape searching

Indexed keywords

KNOWLEDGE BASED SYSTEMS; LIGANDS; MOLECULES; PROTEINS; STOCHASTIC SYSTEMS;

BIOACTIVE CONFORMATION; CONFORMATIONAL SAMPLINGS; CONFORMER GENERATION; DOCKING; KNOWLEDGE-BASED APPROACH; LOWER ENERGIES; PHARMACOPHORES; SAMPLING METHOD; SHAPE-SEARCHING; STOCHASTICS;

CONFORMATIONS;

ACCURACY; ARTICLE; BIOINFORMATICS; COMPLEX FORMATION; COMPUTER PROGRAM; CONFORMATION; CONTROLLED STUDY; DATA EXTRACTION; INTERMETHOD COMPARISON; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN DOMAIN; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; STOCHASTIC MODEL;

EID: 50249126705     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-007-9156-5     Document Type: Article

References (42)

1. Smellie A, Teig SL, Towbin P (1995) J Comp Chem 16:171-187
2. Cato SJ (2000) In: Güner O (ed) Pharmacophore perception, development, use in drug design. International University Line, La Jolla CA, pp 107-125
3. Beusen DD, Shands EFB, Karasek SF, Marshall GR, Dammkoehler RA (1996) J Mol Struct: Theochem 370:157-171
4. Sadowski J, Gasteiger J, Klebe G (1994) J Chem Inf Comput Sci 34:1000-1008
5. Meng EC, Shoichet BK, Kuntz ID (1992) J Comp Chem 13:505-524
6. Venkatachalam CM, Jiang X, Oldfield T, Waldman M (2003) J Mol Graph Model 21:289-307
7. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) J Med Chem 47:1739-1749
8. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) J Mol Biol 267:727-748
9. Jones G, Willett P, Glen RC (1995) J Comput-Aided Mol Des 9: 532-549
10. Hurst T (1994) J Chem Inf Comput Sci 34:190-196
11. Jain AN (2003) J Med Chem 46:499-511
12. Smellie A, Kahn SD, Teig SL (1995) J Chem Inf Comput Sci 35:285-294
13. Martin YC, Bures MG, Danaher EA, DeLazzer J, Lico I, Pavlik PA (1993) J Comput-Aided Mol Des 7:83-102
14. Smellie A, Kahn SD, Teig SL (1995) J Chem Inf Comput Sci 35:295-304
15. CONFORT® was developed by R.S. Pearlman and R. Balducci at the University of Texas, Austin, and is distributed by Tripos International, 1699 S. Hanley Rd., St. Louis MO 63144 USA (http://www.tripos.com)
16. SYBYL® and GALAHAD™ are distributed by Tripos International, 1699 S Hanley Rd, St. Louis MO 63144 USA (http://www.tripos.com)
17. OMEGA is a product of OpenEye Science Software, 3600 Cerrillos Road Suite 1107, Santa Fe NM 87508 USA (http://www.eyesopen.com)
18. Vieth M, Hirst JD, Brooks CL III (1998) J Comput-Aided Mol Des 6:563-572
19. Perola E, Charifson PS (2004) J Med Chem 47:2499-2510
20. Boström J, Norrby P-O, Liljefors T (1998) J Comput-Aided Mol Des 12:383-396
21. Boström J (2001) J Comp-Aided Mol Des 15:1137-1152
22. Strizhev A, Wolohan P, Choi S, Abrahamian E, Clark RD (2006) J Chem Inf Model 46:1862-1870
23. KBProf and KBConf are trademarks of Tripos L.P
24. Nissink JW, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R (2002) Proteins 49:457-471
25. Ash S, Cline MA, Homer RW, Hurst T, Smith GB (1997) J Chem Inf Comput Sci 37:71-79
26. Homer RW, Clark RD, Hurst T, Jilek RJ, Swanson: SYBYL Line Notation (SLN): A single notation to represent chemical structures, queries, reactions, virtual libraries (manuscript in preparation)
27. For details, see http://www.tripos.com/mol2/atom_types.html
28. LeadQuest® is a available from Tripos Discovery Research Centre, Bude-Stratton Business Park, Bude Cornwall EX23 BLY UK (http://www.leadquest.com)
29. Halgren TA (1996) J Comp Chem 17:490-641
30. Halgren TA (1999) J Comp Chem 20:720-748
31. Takahashi Y, Sukekawa M, Sasaki S-I (1992) J Chem Inf Comput Sci 32:639-643
32. Gillet VJ, Willett P, Bradshaw J (2003) J Chem Inf Comput Sci 43:338-345
33. Rarey M, Dixon JS (1998) J Comput-Aided Mol Des 12:471-490
34. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucl Acids Res 28:235-242 (http://www.rcsb.org/pdb)
35. http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/index.html
36. CONCORD® was developed by R.S. Pearlman, A. Rusinko, J.M. Skell and R. Baducci at the University of Texas, Austin, and is distributed exclusively by Tripos International, 1699 S. Hanley Rd., St. Louis MO 63144
37. Boström J, Greenwood JR, Gottfries J (2001) J Mol Graph Model 21:449-462
38. McMartin C, Bohacek R (1997) J Comput-Aided Mol Des 11:333-344
39. Kirchmair J, Wolber G, Laggner C, Langer T (2006) J Chem Inf Model 46:1848-1861
40. Sadowski J, Boström J (2006) J Chem Inf Model 46:2305-2309
41. Klebe G, Mietzner T (1994) J Comput-Aided Mol Des 8:583-606
42. Krystek SR Jr, Hunt JT, Stein PD, Stouch TR (1995) J Med Chem 38:659-668