Introduction — Patterns, Predictions and Problems

  • W. R. Taylor
Conference paper
Part of the Springer Series in Biophysics book series (BIOPHYSICS, volume 7)


The revolution in molecular biology in the seventies began an explosion in the elucidation of biological sequence data that has revealed the sequences of many familiar proteins and many more new proteins, often of unknown function. One of the pressing problems in molecular biology is how to interpret these data to allow informed progress in the study of the proteins whose sequences have been determined. If a new sequence has a clear similarity to a protein of known function (and perhaps even structure) then much can be learnt very rapidly by simply recognising the homology. However, all too often a search across the sequence databanks returns no significant match or perhaps only a match to an equally un-characterised protein. Faced with this situation, two lines can be pursued: one is to look for fragmentary similarities with other proteins rather than search for a similarity over the whole of the new sequence and the other is to attempt to predict the structure of the new protein. Both approaches rely on identifying characteristic sequence patterns and where possible, relating these to known structures.


Pattern Match Protein Structure Prediction Triosephosphate IsoMerase Match Tool Ultimate Rationale 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Dorit, R. L., Schoenbach, L., and Gilbert, W. (1990). How big is the universe of exons? Science, 250: 1377–1382.PubMedCrossRefGoogle Scholar
  2. Lim, V. I. (1974a). Algorithms for the prediction of a-helical and β-structural regions in globular proteins. J. Mol. Biol., 88: 873–894.PubMedCrossRefGoogle Scholar
  3. Lim, V. I. (1974b). Structural principles of the globular organisation of protein chains. A stereochemical theory of globular protein secondary structure. J. Mol. Biol., 88: 857–872.PubMedCrossRefGoogle Scholar
  4. Needleman, S. B. and Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino-acid sequence of two proteins. J. Mol. Biol., 48: 444–453.CrossRefGoogle Scholar
  5. Pearl, L. H. and Taylor, W. R. (1987). A structural model for the retroviral proteases. Nature, 328: 351–354.CrossRefGoogle Scholar
  6. Rawlings, C. J., Taylor, W. R., Nyakairu, J., Fox, J., and Sternberg, M. J. E. (1985). Reasoning about protein topology using the logic programming language PRO-LOG. J. Mol. Graphics, 3: 151–157.CrossRefGoogle Scholar
  7. Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Adv. Prot. Chem., 34: 167–336.CrossRefGoogle Scholar
  8. Smith, R. F. and Smith, T. F. (1990). Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natnl. Acad. Sci. USA, 87: 118–122.CrossRefGoogle Scholar
  9. Taylor, W. R. (1986). Identification of protein sequence homology by consensus sequence alignment. J. Mol. Biol., 188: 233–258.PubMedCrossRefGoogle Scholar
  10. Taylor, W. R. (1991). A template based method of pattern matching in protein sequences. Prog. Biophys. Mol. Biol., 54:159–252. In press.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1992

Authors and Affiliations

  • W. R. Taylor
    • 1
  1. 1.Laboratory of Mathematical BiologyNational Institute for Medical ResearchLondonUK

Personalised recommendations