In Silico Lead Optimization

Chemoinformatics in Drug Discovery

Volumn 23, Issue , 2005, Pages 199-219

  Ho, Chris M W ^a  

^a Drug Design Methodologies LLC   (United States)

Author keywords

Computer aided drug refinement; Development of a component specification language; Filtration of components; in silico lead optimization; Intelligent component selection system; RACHEL Software; Scoring functions; Target functions; Template driven structure generation

Indexed keywords

LIGANDS; SPECIFICATION LANGUAGES;

COMPONENT SPECIFICATION; COMPUTER AIDED; INTELLIGENT COMPONENTS; LEAD OPTIMIZATION; SCORING FUNCTIONS; STRUCTURE GENERATION; TARGET FUNCTIONS;

SPECIFICATIONS;

EID: 77954804619     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/3527603743.ch8     Document Type: Chapter

References (12)

1. HO, C.M.W. RACHEL, RACHEL is developed by Drug Design Methodologies LLC, http://www.newdrugdesign.com and is distributed by Tripos Inc, http://www.tripos.com, 2002.
2. OPREA, T.I., HO, C.M.W., and MARSHALL, G.R. De Novo design: ligand construction and prediction of affinity. In Computer Aided Molecular Design, REYNOLDS, C.H., HOLLOWAY, M.K., and COX, H. (Eds). American Chemical Society, Washington, DC, 1995, 64-81.
3. LINUSSON, A., GOTTFRIES, J., LINDGREN, F., and WOLD, S. Statistical molecular design of building blocks for combinatorial chemistry. J. Med. Chem. 2000, 43, 1320-1328.
4. HO, C.M.W. and MARSHALL, G.R. DBMAKER: A set of programs to generate three-dimensional databases based upon user-specified criteria. J. Comput.-Aided Mol. Des. 1995, 9, 65-86.
5. MUEGGE, I. and ENYEDY, I. Docking and scoring. In Computational Medicinal Chemistry and Drug Discovery, TOLLENAERE, J.DEWINTER, H. LANGENAEKER, W., and BULTINCK, P. (Eds). Marcel Dekker, New York, 2004, 405-436.
6. LEO, A. Estimating LogPoct from structures. Chem. Rev. 1993, 5, 1281-1306.
7. WOLD, S., RUHE, A., WOLD, H., and DUNN, W.J. The collinearity problem in linear regression. The partial least squares approach to generalized inverses. J. Sci. Stat. Comput. 1984, 5, 735-743.
8. HEAD, R.D., SMYTHE, M.L., OPREA, T.I., WALLER, C.L., GREENE, S.M., and MARSHALL, G.R. VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc. 1996, 118, 3959-3969.
9. AJAY and MURCKO, M. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 1995, 38, 4953-4967.
10. MARSHALL, G.R., HEAD, R.D., and RAGNO, R. Affinity prediction: the sine qua non. In Thermodynamics in Biology, DI CERA, E. (Ed.). Oxford University Press, New York, 2000, 87-111.
11. BANNER, D.W. and HADVARY, P. Crystallographic analysis at 3.0 angstroms resolution of the binding to human thrombin of four active site-directed inhibitors. J. Biol. Chem. 1991, 266, 20085-20090.
12. The Protein Data Bank is available from http://www.rcsb.org/pdb.