Turn prediction in proteins using a pattern-matching approach

Biochemistry. 1986 Jan 14;25(1):266-75. doi: 10.1021/bi00349a037.

Abstract

We extend the use of amino acid sequence patterns [Cohen, F.E., Abarbanel, R. M., Kuntz, I. D., & Fletterick, R. J. (1983) Biochemistry 22, 4894-4904] to the identification of turns in globular proteins. The approach uses a conservative strategy, combined with a hierarchical search (strongest patterns first) and length-dependent masking, to achieve high accuracy (95%) on a test set of proteins of known structure. Applying the same procedure to homologous families gives a 90% success rate. Straightforward changes are suggested to improve the predictive power. The computer program, written in Lisp, provides a general pattern-recognition language well suited for a number of investigations of protein and nucleic acid sequences.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence*
  • Computers*
  • Models, Biological
  • Protein Conformation*
  • Proteins*
  • Software*
  • Structure-Activity Relationship

Substances

  • Proteins