Permuting input for more effective sampling of 3D conformer space

Journal of Computer-Aided Molecular Design

Volumn 20, Issue 3, 2006, Pages 179-190

  Carta, Giorgio ^a   Onnis, Valeria ^a   Knox, Andrew J S ^a   Fayne, Darren ^a   Lloyd, David G ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

Conformers; Docking; Drug discovery; Fingerprints; Scoring; SMILES; Virtual screening

Indexed keywords

PRINCIPAL COMPONENT ANALYSIS;

CHEMICAL DATABASE; CHEMICAL SPACE; CONFORMER; CONNECTION TABLE; DOCKING; DRUG DISCOVERY; FINGERPRINT; SCORING; SMILES; VIRTUAL SCREENING;

MOLECULES;

ARABINOSE BINDING PROTEIN; BINDING PROTEIN; CARBONATE DEHYDRATASE; CARBOXYPEPTIDASE; CYCLIN DEPENDENT KINASE; CYTOCHROME P450; DIHYDROFOLATE REDUCTASE; GLUCOCORTICOID; GLUTATHIONE TRANSFERASE; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR AGONIST; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; PHOSPHATASE; PHOSPHOLIPASE A2; PROTEINASE; RETINOIC ACID BINDING PROTEIN; RIBOSOME INACTIVATING PROTEIN; STREPTAVIDIN; THERMOLYSIN; TRYPSIN; TYROSINE PHOSPHATASE; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DRUG DESIGN; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MATHEMATICAL COMPUTING; MOLECULAR MODEL; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN DATA BANK; RELIABILITY; REPRODUCIBILITY; THREE DIMENSIONAL IMAGING;

EID: 33747675478     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-006-9044-4     Document Type: Article

References (26)

1. Hou T, Xu X (2004) Curr Pharm Des 10(9):1011
2. Liao C, Liu B, Shi L, Zhou J, Lu XP (2005) Eur J Med Chem 40(7):632
3. Bringmann BKA (2004) Frequent SMILES. Lernen, Wissensentdeckung und Adaptivität, Workshop GI Fachgruppe Maschinelles Lernen, part of LWA 2004
4. Weininger D (1988) J Chem Inf Comput 28:31
5. Knox AJS, Meegan MJ, Carta G, Lloyd DG (2005) J Chem Inf Model 45(6):1908-19
6. Vigers GP, Rizzi JP (2004) J Med Chem 47(1):80-89
7. Kauppi B, Jakob C, Farnegardh M, Yang J, Ahola H, Alarcon M, Calles K, Engstrom O, Harlan J, Muchmore S, Ramqvist AK, Thorell S, Ohman L, Greer J, Gustafsson JA, Carlstedt-Duke J, Carlquist M (2003) J Biol Chem 278(25):22748
8. Cronet P, Petersen JF, Folmer R, Blomberg N, Sjoblom K, Karlsson U, Lindstedt EL, Bamberg K (2001) Structure (Camb) 9(8):699
9. Daylight Chemical Informations Systems Inc. (URL: Http://www.daylight.com)
10. Molecular Operating Environment (MOE), developed and distributed by Chemical Computing Group (http://wwwchemcompcom)
11. Babel v2.0A3, distributed by Openeye Scientific Software
12. Chemsketch v8.17, www.acdlabs.com
13. Rarey M, Kramer B, Lengauer T, Klebe G (1996) J Mol Biol 261(3):470
14. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) J Mol Biol 267(3):727
15. CORINA 3.6, distributed by Molecular Networks GmbH
16. Cambridge Structural Database, http://www.ccdc.cam.ac.uk/
17. OMEGA 1.8.1, distributed by Openeye Scientific Software
18. Catalyst v4.9.1, www.accelrys.com
19. RUBICON, distributed by Daylight Chemical Informations Systems Inc
20. Shanno DF, Phua KH (1980) ACM Trans Math Software 6:618
21. Bostrom J, Greenwood JR, Gottfries J (2003) J Mol Graph Model 21(5):449
22. Bostrom J (2001) J Comput Aided Mol Des 15(12):1137
23. Ivanciuc O (2003) In: Gasteiger J (ed) Handbook of chemoinformatic, vol. 1. p 103
24. Kudo Y, Sasaki S (1974) J Chem Document 14(4):200
25. Babel 1.100.2, Distributed by Openeye Scientific Software
26. oechem, RMSD, Distributed by Openeye Scientific Software