Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection?

Journal of Computer-Aided Molecular Design

Volumn 22, Issue 3-4, 2008, Pages 169-178

  Good, Andrew C ^a   Oprea, Tudor I ^b  

^a University of New Mexico School of Medicine ^*  (United States)

^b UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

Analogue bias; Chemotypes; DUD; Enrichment; Validation; Virtual screening; WOMBAT

Indexed keywords

SOFTWARE ENGINEERING;

ANALOG BIAS; CHEMOTYPES; DUD; ENRICHMENT; OPTIMISATIONS; PERFORMANCE; TOOL SELECTION; VALIDATION; VIRTUAL SCREENING; WOMBAT;

BENCHMARKING;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL VARIABLE; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN TARGETING; SCREENING TEST; STATISTICAL ANALYSIS; VIRTUAL SCREENING;

EID: 41349122416     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-007-9167-2     Document Type: Article

References (45)

1. Gruneberg S, Wendt B, Klebe G (2001) Angew Chem Int Ed Engl 40:389
2. Wu JH, Batist G (2001) Anticancer Drug Design 16:129
3. Paiva AM, Vanderwall DE, Blanchard JS, Kozarich JW, Williamson JM, Kelly TM (2001) Biochim Biophys Acta 1545:67
4. Perola E, Xu K, Kollmeyer TM, Kaufmann SH, Prendergast FG, Pang Y-P (2000) J Med Chem 43:401
5. Evers A, Klebe G (2004) J Med Chem 47:5381
6. Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK (2002) J Med Chem 45:2213
7. Brenk R, Naerum L, Gradler U, Gerber H-D, Garcia GA, Reuter K, Stubbs MT, Klebe G (2003) J Med Chem 46:1133
8. Kitchen DB, Deconrez H, Furr JR, Bajorath J (2004) Nat Rev Drug Discov 3:935
9. Alvarez JC (2004) Curr Opin Chem Biol 8:365
10. Shoichet BK (2004) Nature 432:862
11. Barril X, Hubbard RE, Morley SD (2004) Mini Rev Med Chem 4:779
12. Jansen JM, Martin EJ (2004) Curr Opin Chem Biol 8:359
13. Krovat EM, Steindl T, Langer T (2005) Curr Comput Aided Drug Des 1:93
14. Mohan V, Gibbs AC, Cummings MD, Jaeger EP, DesJarlais RL (2005) Curr Pharm Des 11:323
15. Rajamani R, Good AC (2007) Curr Opin Drug Discov Devel 10:308
16. Charifsen PS, Corkery JJ, Murcko MA, Patrick Walters W (1999) J Med Chem 42:5100
17. Bissantz C, Folkers G, Rognan D (2000) J Med Chem 43:4759
18. Miteva MA, Lee WH, Montes MO, Villoutriex BO (2005) J Med Chem 48:6012
19. Cummings MD, DesJarlais RL, Gibbs AC, Mohan V, Jaeger EP (2005) J Med Chem 48:962
20. Evers A, Hessler G, Matter H, Klabunde T (2005) J Med Chem 48:5448
21. Chen H, Lyne PD, Giordanetto F, Lovell T, Li J (2006) J Chem Inf Model 46:401
22. Warren GL, Andrews CW, Cappelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS (2006) J Med Chem 49:5912
23. McGaughey GB, Sheridan RP, Bayly CI, Culberson JC, Kreatsoulas C, Lindsley S, Maiorov V, Truchon J-F, Cornell WD (2007) J Chem Inf and Model 47:1504
24. Huang N, Shoichet BK, Irwin JJ (2006) J Med Chem 49:6789
25. http://www.dud.docking.org/10/07
26. Olah M, Mracec M, Ostopovici L, Rad R, Bora A, Hadaruga N, Olah I, Banda M, Simon Z, MracWc M, Oprea TI (2004) In: Oprea TI (ed) WOMBAT: world of molecular bioactivity, in chemoinformatics in drug discovery. Wiley-VCH, New York, pp 223-239
27. http://www.sunsetmolecular.com/products/?id=410/07
28. http://www.dud.docking.org/wombat/accessed 10/07
29. LIGPREP, developed and distributed by Schrodinger Inc.: http://www.schrodinger.com/ProductDescription.php?mID= 6&sID=7&cID=0 10/07
30. Sadowski J, Gasteiger J (1993) J Chem Rev 7:2567
31. Pearlman RS (1987) Chem Des Autom News 2:5
32. ROCS, OMEGA and the OECHEM toolkit are all developed and distributed by Openeye Scientific Software Inc: http://www.eyesopen.com/products 10/07
33. Pipeline Pilot, developed by Scitegic: http://www.scitegic.com/10/07
34. Hawkins PCD, Skillman AG, Nicholls A (2007) J Med Chem 50:74
35. Pham TA, Jain AN (2006) J Med Chem 49:5856
36. http://www.biopharmics.com/downloads.html accessed 11/07
37. Steindl T, Langer T (2004) J Chem Inf Comput Sci 44:1849
38. Oprea TI, Davis AM, Teague SJ, Leeson PD (2001) J Chem Inf Comput Sci 41:1308
39. Ghose AK, Pritchett A, Crippen GM (1988) J Comput Chem 9:80
40. Barnard JM (1993) J Chem Inf Comput Sci 33:532
41. Gillet VJ, Willett P, Bradshaw J (2003) J Chem Inf Comput Sci 43:346
42. Jain AN (2007) 234th ACS National Meeting, Boston, USA, Aug 19-23, COMP-147
43. Smith R, Hubbard RE, Gschwend DA, Leach AR, Good AC (2003) J Mol Graph Model 22:41
44. Good AC, Hermsmeier MA, Hindle SA (2004) J Comput Aided Mol Des 18:529
45. Oprea TI (2002) J Braz Chem Soc 13:811