MOLMAKER: De novo generation of 3D databases for use in drug design

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 1, 1996, Pages 137-145

  Clark, David E ^a   Firth, Mike A ^a   Murray, Christopher W ^a  

^a Proteus Molecular Design Ltd   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CALCINEURIN; CALMODULIN BINDING PROTEIN; CARRIER PROTEIN; ISOMERASE; LIGAND; PEPTIDYLPROLYL ISOMERASE; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN KINASE C;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; DRUG DESIGN; FACTUAL DATABASE; METABOLISM;

AMINO ACID ISOMERASES; CALCINEURIN; CALMODULIN-BINDING PROTEINS; CARRIER PROTEINS; DATABASES, FACTUAL; DRUG DESIGN; LIGANDS; MOLECULAR STRUCTURE; PEPTIDYLPROLYL ISOMERASE; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN KINASE C; SOFTWARE;

EID: 0029687909     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9502055     Document Type: Article

References (53)

1. Bures, M. G.; Martin, Y. C.; Willett, P. Searching Techniques for Databases of Three-Dimensional Chemical Structures. Topics in Stereochemistry 1994, 21, 467-511.
2. Murrall, N. W.; Davies, E. K. Conformational Freedom in 3-D Databases. 1. Techniques. J. Chem. Inf. Comput. Sci. 1990, 30, 312-316.
3. Clark, D. E.; Jones, G.; Willett, P.; Kenny, P. W.; Glen, R. C. Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures Comparison of Conformational-Searching Algorithms for Flexible Searching. J. Chem. Inf. Comput. Sci. 1994, 34, 197-206.
4. Hurst, T. Flexible 3D Searching: The Directed Tweak Technique. J. Chem. Inf. Comput. Sci. 1994, 34, 190-196.
5. Moock, T. E.; Henry, D. R.; Ozkabak, A. G.; Alamgir, M. Conformational Searching in ISIS/3D Databases. J. Chem. Inf. Comput. Sci. 1994, 34, 184-189.
6. Mason, J. S. Experiences with Searching for Molecular Similarity in Conformationally Flexible 3D Databases. In Molecular Similarity in Drug Design; Dean, P. M., Ed.; Blackie, Academic & Professional: London, 1995; pp 138-162.
7. Lam, P. Y. S.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner. M. M.; Wong, Y. N.; Chang, C.-H.; Weber, P. C.; Jackson, D. A.; Sharpe, T. R.; Erickson-Viitanen, S. E. Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors. Science 1994, 263, 380-384.
8. Wang, S.; Zaharevitz, D. W.; Sharma, R.; Marquez, V. E.; Lewin, N. E.; Du, L.; Blumberg, P. M.; Milne, G. W. A. The Discovery of Novel, Structurally Diverse Protein Kinase C Agonists through Computer 3-D Database Pharmacophore Search. Molecular Modelling Studies. J. Med. Chem. 1994, 57, 4479-4489.
9. Kiyama, R.; Homma, T.; Hayashi, K.; Ogawa, M.; Hara, M.; Fujimoto, M.; Fujishita, T. Novel Angiotensin II Receptor Antagonists: Design, Synthesis and In Vitro Evaluation of Dibenzo[a,d]cycloheptene and Dibenzo[b,f]oxepin Derivatives. Searching for Bioisosteres of Biphenylyltetrazole using a Three-Dimensional Search Technique. J. Med. Chem. 1995, 38, 2728-2741.
10. Rusinko, III, A.; Skell, J. M.; Balducci, R.; McGarity, C. M.; Pearlman, R. S. Concord: A Program for the Rapid Generation of High Quality Approximate 3-Dimensional Molecular Structures; The University of Texas at Austin and Tripos Associates: St. Louis, MO, 1988.
11. Chem-X; Chemical Design Ltd.: Roundway House, Cromwell Park, Chipping Norton, Oxfordshire, OX7 5SR.
12. Alien, F. H.; Davies, J. E.; Galloy, J. J.; Johnson, O.; Kennard, O.; Macrae, C. F.; Mitchell, E. M.; Mitchell, E. F.; Smith, J. M.; Watson, D. G. The Development of Versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 1991, 31, 187-204.
13. Gallop, M. A.; Barrett, R. W.; Dower, W. J.; Fodor, S. P. A.; Gordon, E. M. Applications of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries. J. Med. Chem. 1994, 37, 1233-1251.
14. Gordon, E. M.; Barrett, R. W.; Dower, W. J., Fodor, S. P. A.; Gallop, M. A. Applications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future Directions. J. Med. Chem. 1994, 37, 1385-1401.
15. van Drie, J. H. 3D Database Searching in Drug Discovery. Network Science (http://www.awod.com/netsci) 1995, 1, Issue 4 (October).
16. Nilakantan, R.; Bauman, N.; Venkataraghavan, R. A Method for Automatic Generation of Novel Chemical Structures and Its Potential Applications to Drug Discovery. J. Chem. Inf. Comput. Sci. 1991, 31, 527-530.
17. Martin, Y. C.; Van Drie, J. H. Identifying Unique Core Molecules from the Output of a 3D Database Search. In Chemical Structures 2. The International Language of Chemistry; Warr, W. A., Ed.; Springer Verlag: Berlin, 1993; pp 315-326.
18. Weininger, D. SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-38.
19. Martin, Y. C. 3D Database Searching in Drug Design. J. Med. Chem. 1992, 35, 2145-2154.
20. Martin, Y. C. Computer Design of Potentially Bioactive Molecules by Geometric Searching with ALADDIN. Tetrahedron Comput. Methodol. 1990, 3, 15-25.
21. Ho, C. M. W.; 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, 69-86.
22. Glen, R. C.; Payne, A. W. R. A Genetic Algorithm for the Automated Generation of Molecules within Constraints. J. Comput.-Aided Mol. Des. 1995, 9, 181-202.
23. Lauri, G.; Bartlett, P. A. CAVEAT: A Program to Facilitate the Design of Organic Molecules. J. Comput.-Aided Mol. Des. 1994, 8, 51-66.
24. Alberg, D. G.; Schreiber, S. L. Structure-Based Design of a Cyclophilin-Calcineurin Bridging Ligand. Science 1993, 262, 248-250.
25. Weiss, G. A.; Collins, E. J.; Garboczi, D. N.; Wiley, D. C.; Schreiber, S. L. A Tricyclic Ring System Replaces the Variable Regions of Peptides by Three Alleles of Human MHC Class I Molecules. Chem. Biol. 1995, 2, 401-407.
26. Hall, L. H.; Fisk, J. B. Computer Generation of Vertex Degree Sets for Chemical Graphs from a Number of Vertices and Rings. J. Chem. Inf. Comput. Sci. 1994, 34, 1184-1188.
27. Kier, L. B.; Hall, L. H.; Frazer, J. W. Design of Molecules from Quantitative Structure-Activity Relationship Models. 1. Information Transfer between Path and Vertex Degree Counts. J. Chem. Inf. Comput. Sci. 1993, 33, 143-147.
28. Hall, L. H.; Kier, L. B.; Frazer, J. W. Design of Molecules from Quantitative Structure-Activity Relationship Models. 2. Derivation and Proof of Information Transfer Relating Equations. J. Chem. Inf. Comput. Sci. 1993, 33, 148-152.
29. Hall, L. H.; Kier, L. B. Design of Molecules from Quantitative Structure-Activity Relationship Models. 3. Role of Higher Order Path Counts. J. Chem. Inf. Comput. Sci. 1993, 33, 598-603.
30. Kvasnička, V.; Pospíchal, J. An Improved Method of Constructive Enumeration of Graphs. J. Math. Chem. 1992, 9, 181-196.
31. Kvasnička, V.; Pospíchal, J. An Improved Version of the Constructive Enumeration of Molecular Graphs with Prescribed Sequence of Valence States. Chemom. Intell. Lab. Syst. 1993, 18, 171-181.
32. Pospíchal, J.; Kvasnička, V. An Alternative Approach for Constructive Enumeration of Graphs. Collect Czech. Chem. Commun. 1993, 58, 754-774.
33. Yang, Y.-Q.; Xu, L.; Hu, C.-Y. Extended Adjacency Matrix Indices and Their Applications. J. Chem. Inf. Comput. Sci. 1994, 34, 1140-1145.
34. Reference deleted in proof.
35. Reference deleted in proof.
36. Dalby, A.; Nourse, J. G.; Hounshell, W. D.; Gushurst, A. K. I.; Grier, D.; Leland, B. A.; Laufer, J. Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Ltd. J. Chem. Inf. Comput. Sci. 1992, 32, 244-255.
37. Pearlman, R. S. 3D Molecular Structures: Generation and Use in 3D Searching. In 3D QSAR in Drug Design: Theory, Method and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, 1993; pp 41-79.
38. Ricketts, E. M.; Bradshaw, J.; Hann, M.; Hayes, F.; Tanna, N. Comparison of Conformations of Small Molecule Structures from the Protein Data Bank with Those Generated by Concord, Cobra, ChemDBS-3D and Converter and Those Extracted from the Cambridge Structural Database. J. Chem. Inf. Comput. Sci. 1993, 33, 905-925.
39. Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures. J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008.
40. Converter, Version 2.3; Biosym/MSI: San Diego, CA.
41. Havel, T. F. An Evaluation of Computational Strategies for Use in the Determination of Protein Structure from Distance Constraints Obtained by Nuclear Magnetic Resonance. Prog. Biophys. Mol. Biol. 1991, 56, 43-78.
42. Sketch and Converter User Guide, Version 2.3; Biosym/MSI: San Diego, CA, 1993.
43. ISIS/3D, Version 1.2; MDL Information Systems Inc.: San Leandro, CA.
44. Search_Compare, Version 2.3; Biosym/MSI: San Diego, CA, 1993.
45. As implemented in the program Discover, Version 2.9.5; Biosym/MSI: San Diego, CA, 1993.
46. Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K. Atomic Physicochemical Parameters for Three-Dimensional Structure Directed Quantitative Structure-Activity Relationships. 4. Additional Parameters for Hydrophobic and Dispersive Interactions and their Application for an Automated Superposition of Certain Naturally Occurring Nucleoside Antibodies. J. Chem. Inf. Comput. Sci. 1989, 29, 163-172.
47. Ke, H.; Mayrose, D.; Belshaw, P. J.; Alberg, D. G.; Schreiber, S. L.; Chang, Z. Y.; Etzkorn, F. A.; Ho, S.; Walsh, C. T. Crystal Structures of Cyclophilin A Complexed with Cyclosporin A and N-methyl-4-[(E)-3-butenyl]-4,4-dimethylthreonine Cyclosporin A. Structure 1994, 2, 33-44.
48. Fesik, S. W.; Gampe Jr., R. T.; Eaton, H. L.; Gemmecker, G.; Olejniczak, E. T.; Neri, P.; Holzman, T. F.; Egan, D. A.; Edalji, R.; Simmer, R.; Helfrich, R.; Hochlowski, J.; Jackson, M. NMR Studies of (u-13c)Cyclosporin A Bound to Cyclophilin: Bound Conformation and Portions of Cyclosporin Involved in Binding. Biochemistry 1991, 30, 6574-6583.
49. Insight II, Version 2.3.0; Biosym/MSI: San Diego, CA.
50. Johnson, A. P. New Developments in the SPROUT Program for De Novo Design and the CAESA System for Estimation of Synthetic Accessibility. Presented at the 13th Annual Conference of the Molecular Graphics Society, Evanston, IL, July 1994.
51. Grund, R. Construction of molecular graphs with given hybridization and non-overlapping fragments. Bayreuther Mathematische Schriften 1995, 49, 1-113. (In German).
52. Faradzhev, I. Generation of Nonisomorphic Graphs with Given Partition of Vertex Degrees. In Algorithmic Investigations in Combinatorics; Faradzhev, I., Ed.; Nauka: Moscow, 1978; pp 11-19 (in Russian).
53. ACD: Available Chemicals Directory Release 94.2, MDL Information Systems Inc.: San Leandro, CA.CI9502055