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Using Prolog to represent and reason about protein structure

  • C. J. Rawlings
  • W. R. Taylor
  • W. R. Taylor
  • J. Nyakairu
  • J. Fox
  • M. J. E. Sternberg
Session 5b: Applications And Teaching
Part of the Lecture Notes in Computer Science book series (LNCS, volume 225)

Abstract

Logic programming methods have been used to represent and reason about protein structural topology. A description of the relative positions (the topology) of protein structural features enabled declarative representations of super-secondary structures to be used to search for structural motifs. An important feature of this approach is the ability to reason symbolically about complex topological structures in terms of a small set of simple spatial relationships.

Keywords

Tomato Bushy Stunt Virus Protein Topology Topological Reasoning Imperial Cancer Research Fund Prolog Clause 
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.

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References

  1. 1.
    Richardson, J. (1977) β-Sheet Topology and the Relatedness of proteins Nature, 268, 495–500PubMedGoogle Scholar
  2. 2.
    Cohen, F.E., Sternberg, M.J.E., Taylor, W.R. (1982) Analysis and Prediction of the Packing of α-Helices against a β-Sheet in the Tertiary Structure of Globular Proteins Journal of Molecular Biology, 156, 821–862PubMedGoogle Scholar
  3. 3.
    Taylor, W.R., Thornton, J.M. (1983) Prediction of Super-Secondary Structure in Proteins Nature, 301, 540–542PubMedGoogle Scholar
  4. 4.
    Rawlings, C.J., Taylor, W.R., Nyakairu, J., Fox, J., Sternberg, M.J.E. (1985) Reasoning About Protein Topology Using the Logic Programming Language Prolog J. Mol. Graphics, 3, 151–157Google Scholar
  5. 5.
    Sternberg, M.J.E., Thornton, J.M. (1977) On the Conformation of Proteins: The Handedness of the Connection between Parallel β-Strands Journal of Molecular Biology, 110, 269–283PubMedGoogle Scholar
  6. 6.
    Bernstein, F.C., Koetzle, T., William, G.J.B., Meyer, E. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. (1977) The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures Journal of Molecular Biology, 112, 535–542PubMedGoogle Scholar
  7. 7.
    Kowalski, R (1979) Logic for Problem Solving In: Artificial Intelligence Series, 7, North Holland Press, AmsterdamGoogle Scholar
  8. 8.
    Ptitsyn, O.B., Finkelstein, A.V. (1980) Similarities of Protein Topologies: Evolutionary Divergence — Functional Convergence or Principles of Folding? Annual Reviews of Biophysics, 13, 339–386Google Scholar
  9. 9.
    Bowen, D.L., Byrd, L., Pereira, F.C.N., Pereira, L.M., Warren, D.H.D. (1982) DECsystem-10 PROLOG USER'S MANUAL University of Edinburgh, Dept of Artificial IntelligenceGoogle Scholar
  10. 10.
    Futo, I., Darvas, F., Szeredi, P. (1978) The application of Prolog to the development of QA and DBM systems In: Logic and Databases, Eds: Gallaire, H., Minker, J., Plenum PressGoogle Scholar
  11. 11.
    Bundy, A., Byrd,L., Mellish, C. (1982) Special Purpose but Domain Independent Inference Mechanisms Proceedings, European Conference AI, 1982, 67–74Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1986

Authors and Affiliations

  • C. J. Rawlings
    • 1
  • W. R. Taylor
    • 2
  • W. R. Taylor
    • 1
    • 2
  • J. Nyakairu
    • 1
    • 2
  • J. Fox
    • 1
  • M. J. E. Sternberg
    • 2
  1. 1.Biomedical Computing UnitImperial Cancer Research FundLondon
  2. 2.Laboratory of Molecular Biology, Dept. of CrystallographyBirkbeck CollegeLondon

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