Abstract
This paper discusses techniques for chemical substructure searching in files of three-dimensional (3-D) chemical structures. A methodology is presented for the selection of search screens which are based upon interatomic distance information, the use of these screens on a file of 3-D chemical structures taken from the Cambridge Crystallographic Data Bank (CCDB) shows that they allow searches for typical pharmacophoric patterns to be carried out with high efficiency. A range of subgraph isomorphism algorithms is described for geometric searching, the 3-D equivalent of atom-by-atom searching in conventional substructure search systems. Current research involves the development of hardware and software techniques for the identification of the maximal substructures common to sets of 3-D structures, and the extension of the work on substructure searching in the CCDB to the macromolecular structures in the Protein Data Bank.
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Communication, Storage and Retrieval of Chemical Information, Ash, J.E., Chubb, P., Ward, S.E., Welford, S.M., Willett, P., Eds, Ellis Horwood: Chichester, 1985.
Willett, P. ‘A Review of Chemical Structure Retrieval Systems’. J. Chemometrics. In the press.
Wipke, W.T., Dyott, T.M. ‘Stereochemically Unique Naming Algorithm’. J. Am. Chem. Soc. 1974, 96, 4834–4842.
Gund, P., Andose, J.D., Rhodes, J.B, Smith, G.M. ‘Three-dimensional Molecular Modelling and Drug Design’. Science 1980, 208, 1425–1431.
Humblet, C., Marshall, G.R. ‘Three-dimensional Computer Modelling as an Aid to Drug Design’. Drug Dev. Res. 1981, 1, 409–434
Gund, P. ‘Three-dimensional Pharmacophoric Pattern Searching’. Prog. Mol. Subcell. Biol. 1977, 5, 117–143.
Gund, P. ‘Pharmacophore Pattern Searching and Receptor Mapping’. Annu. Rep. Med. Chem. 1979, 14, 299–308.
Dittmar, P.G., Farmer, N.A., Fisanick, W., Haines, R. C, Mockus, J. ‘The CAS ONLINE Search System. I. General System Design and Selection, Generation and Use of Search Screens’. J. Chem. Inf. Comput. Sci. 1983, 23, 93–102.
Kier, L.B. ‘The Prediction of Molecular Conformation as a Biologically Significant Property’. Pure Appl. Chem. 1973, 35, 509–520.
Kelley, J.M., Adamson, R.H. ‘A Comparison of Common Interatomic Distancesin Serotonin and Some Halluginogenic Drugs’. Pharmacology 1973, 10, 28–31.
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.
Adamson, G.W., Cowell, J., Lynch, M.F., McLure, A.H.W., Town, W.G., Yapp, A.M. ‘Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files’. J. Chem. Doc. 1973, 13, 153–157.
Hodes, L. ‘Selection of Descriptors According to Discrimination and Redundancy. Application to Chemical Structure Searching’. J. Chem. Inf. Comput. Sci. 1976, 16, 88–93.
Willett, P. ‘A Screen Set Generation Algorithm’. J. Chem. Inf. Comput. Sci. 1979, 19, 159–162.
Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B.G., Kennard, O., Motherwell, W.D.S., Rogers, J.R., Watson, D.G. ‘The Cambridge Crystallographic Data Centre: Computer-based Search, Retrieval, Analysis and Display of Information’ Acta Crystallogr. B35, 2331–2339
Jakes, S.E., Willett, P. ‘Pharmacophoric Pattern Matching in Files of Three-dimensional Chemical Structures. Selection of Interatomic Distance Screens’. J. Mol. Graphics 1986, 4, 12–20.
Jakes, S.E., Watts, N., Willett, P., Bawden D., Fisher, J.D. ‘Pharmacophoric Pattern Matching in Files of 3-D Chemical Structures: Evaluation of Search Performance’. J. Mol. Graphics. In the press.
Brint, A.T., Willett, P. ‘Pharmacophoric Pattern Matching in Files of 3-D Chemical Structures: Comparison of Geometric Searching Algorithms’. J. Mol. Graphics. In the press.
Lesk, A.M. ‘Detection of 3-D Patterns of Atoms in Chemical Structures’. Commun. ACM 1979, 22, 219–224.
Levi, G. ‘A Note on the Derivation of Maximal Common Subgraphs of Two Directed or Undirected Graphs’. Calcolo 1972, 9, 341–352.
Barrow, H.G., Burstall, R.M. ‘Subgraph Isomorphism, Matching Relational Structures and Maximal Cliques’. Inf. Process. Letts. 1976, 4, 83–84.
Barrow, H.G., Tenebaum, J.M. ‘Computational Vision’. Proc. IEEE 1981, 69, 572–595.
McGregor, J.J. ‘Backtrack Search Algorithms and the Maximal Common Subgraph Problem’. Software Pract. Exper. 1982, 12, 23–24.
Modern Approaches to Chemical Reaction Searching, Willett, P. Ed., Gower: Aldershot, 1986.
Logical and Combinatorial Algorithms for Drug Design, Golender, V., Rosenblit, A., Eds., Research Studies Press: Letch worth, 1983.
Kühl, F.S., Crippen, G.M., Friesen, D.K. ‘A Combinatorial Algorithm for Calculating Ligand Binding’. J. Comput. Chem. 1984, 5, 24–34.
Bron, C., Kerbosch, J. ‘Algorithm 457. Finding all Cliques of an Undirected Graph’. Commun. ACM, 1973, 16, 575–577.
Ullman, J.R. ‘An Algorithm for Subgraph Isomorphism’. J. Assoc. Comput. Mach. 1976, 23, 31–42.
Brint, A.T., Willett, P. ‘Algorithms for the Identification of Three-dimensional Maximal Common Substructures’. Submitted for publication.
Wipke, W.T., Rogers, D. ‘Rapid Subgraph Search Using Parallelism’. J. Chem. Inf. Comput. Sci. 1984, 24, 255–262.
Gillet, V.J., Welford, S.M., Lynch, M.F., Willett, P., Manson, G., Thompson, J. ‘Computer Storage and Retrieval of Generic Chemical Structures in Patents. 7. Parallel Simulation of a Relaxation Algorithm for Chemical Substructure Search’. J. Chem. Inf. Comput. Sci. 1986, 26, 118–126.
Barron, I.M. ‘The Transputer and Occam’. In Information Proceedings 86, Kugler, H.J. Ed., Elsevier: Amsterdam, 1986.
May, D., Taylor, R. ‘Occam - An Overview’. Microprocessors and Microsystems 1984, 8, 73–79.
Kneale, G.G., Bishop, M. J. ‘Nucleic Acid and Protein Sequence Databases’. Comput. Appl. Biosci. 1985, 2, 11–17.
Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison, Sankoff, D., Krusaki, J.B., Eds., Addison-Wesley: Reading, Massachusetts, 1983.
Abola, E.E., Bernstein, F.C., Koetzle, T.F. ‘The Protein Data’. In The Role of Data in Scientific Progress, Glaeser, P.J. Ed., Elsevier: New York, 1985.
Levitt, M., Greer, J. ‘Automatic Identification of Secondary Structure in Globular Proteins’. J. Mol. Biol. 1977, 114, 181–203.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1988 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Brint, A.T., Mitchell, E., Willett, P. (1988). Substructure Searching in Files of Three-Dimensional Chemical Structures. In: Warr, W.A. (eds) Chemical Structures. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-73975-0_14
Download citation
DOI: https://doi.org/10.1007/978-3-642-73975-0_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-73977-4
Online ISBN: 978-3-642-73975-0
eBook Packages: Springer Book Archive