Protein fold recognition from secondary structure assignments

R. B. Russell, R. R. Copley, G. J. Barton

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

A method for finding protein folds consistent with secondary structure assignments and imposed experimental restraints is described. All possible matches between the query pattern and every member of a database of protein structural domains are generated by a comparison of secondary structure assignments. The comparison allows for errors in predicted secondary structure elements and possible variations between query and database structure. Several filters remove matches that are un-compact, that have poor beta/ sheet bonding, that do not allow loop/turn lengths to bridge the distance between connected secondary structures, or that fail to satisfy imposed experimental restraints (e.g. disulphide bonds). The remaining matches provide a set of plausible topologies for a protein of unknown structure, which can be inspected visually or tested by experiment. A search using the src homology 2 domain prediction finds 13 possible topologies, one being a domain from the E. coli bio protein known to adopt an SH2 fold. The use and development of the method are discussed.

Original languageEnglish
Title of host publicationProceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS 1995)
PublisherIEEE
Pages302-311
Number of pages10
ISBN (Electronic)0818669306
DOIs
Publication statusPublished - 1995
Event28th Annual Hawaii International Conference on System Sciences, HICSS 1995 - Wailea, United States
Duration: 3 Jan 19956 Jan 1995

Publication series

NameProceedings of the Annual Hawaii International Conference on System Sciences
Volume5
ISSN (Print)1530-1605

Conference

Conference28th Annual Hawaii International Conference on System Sciences, HICSS 1995
CountryUnited States
CityWailea
Period3/01/956/01/95

Keywords

  • Proteins
  • Databases
  • Topology
  • Laboratories
  • Molecular biophysics
  • Buildings
  • Pattern matching
  • Matched filters
  • Bonding
  • Bridges

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  • Cite this

    Russell, R. B., Copley, R. R., & Barton, G. J. (1995). Protein fold recognition from secondary structure assignments. In Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS 1995) (pp. 302-311). [375326] (Proceedings of the Annual Hawaii International Conference on System Sciences; Vol. 5). IEEE. https://doi.org/10.1109/HICSS.1995.375326