BOOMSLANG: A program for combinatorial structure generation

Journal of Molecular Graphics

Volumn 14, Issue 1, 1996, Pages 1-5

  Cosgrove, David A ^a   Kenny, Peter W ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

Ligand design; Molecular design; Pharmacophore; Structure generation

Indexed keywords

DRUG CARRIER;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; DRUG STRUCTURE; ENERGY; GEOMETRY; MOLECULAR MODEL; PRIORITY JOURNAL;

EID: 0029988211     PISSN: 02637855     EISSN: None     Source Type: Journal    
DOI: 10.1016/0263-7855(95)00040-2     Document Type: Article

References (34)

1. Lewis, R.A., and Leach, A.R. Current methods for sitedirected structure generation. J. Comput.-Aided Mol. Design 1994, 8, 467-475
2. Rotstein, S.H., and Murcko, M.A. GroupBuild: A fragment-based method for de novo drug design. J. Med. Chem. 1993; 36, 1700-1710
3. Böhm, H.-J. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. J. Comput.-Aided Mol. Design 1992, 6, 61-78
4. Bohacek, R.S., and McMartin, C. Highly diverse structures complementary to enzyme binding sites: Results of extensive application of a de novo design method incorporating combinatorial growth. J. Am. Chem. Soc. 1994, 116, 5560-5571
5. Caflisch, A., Miranker, A., and Karplus, M. Multiple copy simultaneous search and construction of ligands in binding sites: Application to inhibitors of HIV-1 aspartic protease. J. Med. Chem. 1993, 36, 2142-2167
6. Marshall, G.R., Barry, C.D., Bosshard, H.E., Dammkoehler, R.A., and Dunn, D.A. The conformational parameter in drug design: The active analogue approach. ACS Symp. Ser. 1979, 112, 205-226
7. Dammkoehler, R.A., Karasek, S.F., Shands, E.F.B., and Marshall, G.R. Constrained search of conformational hyperspace. J. Comput.-Aided Mol. Design 1989, 3, 3-21
8. Martin, Y.C., Bures, M.G., Danaher, E.A., DeLazzer, J., Lico, I., and Pavlik, P.A. A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. J. Comput.-Aided Mol. Design 1993, 7, 83-102
9. Leichtfried, F.E. Novel approaches to high throughput screening automation. In: Proceedings of the First Forum on Data Management Techniques in Biological Screening (Carter, C., and Freter, F.R., eds.). SRI International Menlo Park, California, 1992, pp. 82-86
10. Burch, R.M. Mass ligand binding and screening for receptor antagonists: Prototype new drugs and blind alleys. J. Receptor Res. 1991, 11, 101-113
11. Gallop, M.W., Barrett, R.W., Dower, W.J., Fodor, S.P. A., and Gordon, E.M. Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J. Med. Chem. 1994, 37, 1233-1251
12. Gordon, E.M., Barrett, R.W., Dower, W.J., Fodor, S.P. A., and Gallop, M.W. Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J. Med. Chem. 1994 , 37, 1385-1401
13. Jung, G., and Beck-Sickinger, A.G. Multiple peptide synthesis methods and their applications. Angew. Chem. Int. Ed. Engl. 1992, 31, 367-383
14. Masek, B.B., Merchant, A., and Matthew, J.B. Molecular shape comparison of angiotensin II receptor antagonists. J. Med. Chem. 1993, 36, 1230-1238
15. Connolly, M.L. Computation of molecular volume. J. Am. Chem. Soc. 1985, 107, 1118-1124
16. Böhm, H.-J. The development of a simple scoring function to estimate the binding constant for a protein-ligand complex of known structure. J. Comput.-Aided Mol. Design 1994, 8, 243-256
17. Cramer, III, R.D., Patterson, D.E., and Bunce, J.D. Comparative molecular field analysis (CoMFA). I. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967
18. Moos, W.H., Green, G.D., and Pavia, M.R. Recent advances in the generation of molecular diversity. Annu. Rep. Med. Chem. 1993, 28, 315-324
19. Lauri, G., and Bartlett, P.A. CAVEAT: A program to facilitate the design of organic molecules. J. Comput.-Aided Mol. Design 1994, 8, 51-66
20. Daylight Chemical Information Systems, Inc., Irvine, California
21. Anderson, E., Veith, G.D., and Weininger, D. SMILES, a chemical language and information system. I. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36
22. Martin, Y.C., Bures, M.G., and Willett, P. Searching databases of three-dimensional structures. Rev. Comput. Chem. 1990, 1, 213-263
23. Martin, Y.C. 3D database searching in drug design. J. Med. Chem. 1992, 35, 2145-2154
24. Siani, M.A., Weininger, D., and Blaney, J.M. CHUCKLES: A method for representing and searching peptide and peptoid sequences on both monomer and atomic levels. J. Chem. Inf. Comput. Sci. 1994, 34, 588-593
25. Ho, C.M.W., and Marshall, G.R. DBMAKER: A set of programs to generate three-dimensional databases based on user-specified criteria., J. Comput.-Aided Mol. Design 1995, 9, 65-86
26. TRIPOS Associates, 1699 South Hanley Road. St. Louis, Missouri
27. Weininger, D., Weininger, A., and Weininger, J.L. SMILES. 2. Algorithm for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci. 1989, 29, 97-101
28. Rusinko III, A., Skell, J.M., Balducci, R., McGarity, C.M., and Perlman, R.S. CONCORD: A Program for the Rapid Generation of High Quality Three-Dimensional Structures. The University of Texas at Austin and TRIPOS Associates, 1699 South Hanley Road, St. Louis, Missouri, 1988
29. Nachbar, RB., and Mislow, K. BIGSTRN-3: A general-purpose empirical force-field, QCPE Number 514, Quantum Chemistry Program Exchange, Indiana University, Bloomington, Indiana
30. Allinger, N.L., and Yuh, Y.H. MM2: Molecular Mechanics II, QCPE Number 395, Quantum Chemistry Program Exchange, Indiana University, Bloomington, Indiana
31. Crippen, G.M. Distance Geometry and Conformational Calculations (Bawden, D., ed.). Research Studies Press (Wiley), New York, 1981
32. Crippen, G.M., and Havel, T.F. Distance Geometry and Molecular Conformation (Bawden, D., ed.). Research Studies Press (Wiley), New York, 1988
33. Blaney, J.M., Crippen, G.M., Dearing, A., and Dixon, J.S. DGEOM: Distance geometry, QPCE Number 590, Quantum Chemistry Program Exchange, Indiana University, Bloomington, Indiana
34. Diamond, R. A note on the rotational superposition problem. Acta Crystallogr. 1988, A44, 211-216