GMA: A generic match algorithm for structural homomorphism, isomorphism, and maximal common substructure match and its applications

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 1, 1996, Pages 25-34

  Xu, Jun ^a  

^a BIO RAD LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001970497     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci950061u     Document Type: Article

References (37)

1. Garey, M. R.; Johnson, D. S. Computers and Intractability: a Guide to the Theory of NP-Completeness; W. H. Freeman: San Francisco, 1979.
2. Harel, D. Algorithmics: the Spirit of Computing; Addison-Wesley: Reading, MA, 1987.
3. Ullman, J. R. An Algorithm for Subgraph Isomorphism. J. Assoc. Comput. Machinery 1976, 23, 31-42.
4. Chemical Structures 2; Warr, W. A., Ed.; Springer-Verlag: New York, 1993.
5. Willett, P. Three-Dimensional Chemical Structure Handling; John Wiley & Sons: New York, 1991.
6. Wilson, T. Chemical Searching on an Array Processor; John Wiley & Sons: New York, 1993.
7. Barnard, J. M. Substructure Searching Methods: Old and New. J. Chem. Inf. Comput. Sci. 1993, 33, 532-538.
8. Levi, G. A Note on the Derivation of Maximal Common Subgraphs of Two Directed or Undirected Graphs. Calcolo 1972, 9, 341-352.
9. Barrow, H. G.; Burstall, R. M. Subgraph Isomorphism, Matching Relational Structures and Maximal Cliques. Information Process. Lett. 1976, 4, 83-84.
10. Johnson, M. A.; Maggiora, G. M. Concepts and Applications of Molecular Similarity. John Wiley: New York, 1990.
11. Crandell, C. W.; Smith, D. H. Computer-Assisted Examination of Compounds for Common Three-Dimensional Substructures. J. Chem. Inf. Comput. Sci. 1983, 23, 186-197.
12. McGregor, J. J.; Willet, P. Use of a Maximal Common Subgraph Algorithm in the Automatic Identification of the Ostensible Bond Changes Occurring in Chemical Reactions. J. Chem. Inf. Comput. Sci. 1981, 21, 137-140.
13. Willet, P. Modern Approaches to Chemical Reaction Searching; Aldershot: Gower, 1986.
14. Chen, L.; Robien, W. MCSS: A New Algorithm for Perception of Maximal Common Substructures and Its Applications to NMR Spectral Studies. 1. The Algorithm. J. Chem. Inf. Comput. Sci. 1992, 32, 501-506.
15. Plotkin, M. Mathematical Basis of Ring-finding Algorithms in CIDS. J. Chem. Doc. Comput. Sci. 1971, 11, 60-63.
16. Corey, E. J.; Petersson, G. A. An Algorithm for Machine Perception of Synthetically Significant Rings in Complex Cyclic Organic Structures. J. Am. Chem. Soc. 1972, 94(2), 460-465.
17. Wipke, W. T.; Dyott, T. Use of Ring Assemblies in a Ring Perception Algorithm. J. Chem. Inf. Comput. Sci. 1975, 15, 140-144.
18. Matyska, L. Fast Algorithm for Ring Perception. J. Comput. Chem. 1988, 9, 455-459.
19. Downs, G. M.; Gillet, V. J.; Holliday, J. D.; Lynch, M. F. A Review of Ring Perception Algorithms for Chemical Graphs. J. Chem. Inf. Comput. Sci. 1989, 29, 172-187.
20. Downs, G. M.; Gillet, V. J.; Holliday, J. D.; Lynch, M. F. Theoretical Aspects of Ring Perception, and Development of the Extended Set of Smallest Rings (ESSR) Concept. J. Chem. Inf. Comput. Sci. 1989, 29, 187-206.
21. Downs, G. M.; Gillet, V. J.; Holliday, J. D.; Lynch, M. F. Computer Storage and Retrieval of Generic Chemical Structures in Patents. 9. An Algorithm to Find the Extended Set of Smallest Rings (ESSR) in Structurally Explicit Generics. J. Chem. Inf. Comput. Sci. 1989, 29, 207-214.
22. Cahn, R. S.; Ingold, C.; Prelog, V. Specification of Molecular Chirality. Angew. Chem., Int. Ed. Engl. 1966, 5, 385-551.
23. Prelog, V.; Helmchen, H. Basic Principles of the CIP-System and Proposals for a Revision. Angew. Chem., Int. Ed. Engl. 1982, 21, 567-583.
24. Wipke, W. T.; Dyott, T. M. Simulation and Evaluation of Chemical Synthesis. Computer Representation and Manipulation of Stereochemistry. J. Am. Chem. Soc. 1974, 96, 4825-4834.
25. Blackwood, J. E.; Elliot, P. M.; Stobaugh, R. E.; Watson, C. E. The Chemical Abstracts Service Chemical Registry System III. Stereochemistry. J. Chem. Inf. Comput. Sci. 1977, 17, 3-8.
26. Shelley, C. A.; Munk, M. E. An Approach to the Assignment of Canonical Connection Tables and Topological Symmetry Perception. J. Chem. Inf. Comput. Sci. 1979, 19, 247-250.
27. Mockus, J.; Stobaugh, R. E. Chemical Abstracts Service Chemical Registry System. 7. Tautomerism and Alternating Bonds. J. Chem. Inf. Comput. Sci. 1980, 20, 18-22.
28. Ray, L. C.; Kirsch, R. A. Finding Chemical Records by Digital Computers. Science 1957, 126, 814-819.
29. Xu, J.; Zhang, M. HBA: New Algorithm for Structural Match and Applications. Tetrahedron Comput. Methodol. 1989, 2, 75-83.
30. Dengler, A.; Ugi, I. A Central Atom Based Algorithm and Computer Program for Substructure Search, Comput. Chem. 1991, 15, 103-107.
31. Sussenguth, E. H. A Graph-Theoretic Algorithm for Matching Chemical Structures. J. Chem. Doc. 1965, 5, 36-43.
32. Figueras, J. Substructure Search by Set Reduction. J. Chem. Doc. 1972, 12, 237-244.
33. Von Scholley, A. A Relaxation Algorithm for Generic Chemical Structure Screening. J. Chem. Inf. Comput. Sci. 1984, 24, 235-241.
34. Balaban, A. T., Ed.; Chemical Applications of Graph Theory; Academic Press: New York, 1976; Chapter 11.
35. Pellegrin, V. J. Chem. Educ. 1983, 60, 626.
36. March, J. Advanced Organic Chemistry, 4th ed.; John Wiley & Sons: New York, 1992; 94-123.
37. March, J. Advanced Organic Chemistry, 4th ed.; John Wiley & Sons: New York, 1992; 69-73.