Beta-sheet prediction using inter-strand residue pairs and refinement with Hopfield neural network

Proc Int Conf Intell Syst Mol Biol. 1997:5:48-51.

Abstract

Many secondary prediction methods have been studied, but the prediction accuracy is still unsatisfactory, since beta-sheet prediction is difficult. In this research, we gathered statistics of pairs of three residue sub-sequences in beta-sheets, calculated propensities for them. When a sequence is given, all possible three residue sub-sequences are examined whether they form beta-sheets. A short coming is that many false predictions are made. To exclude false predictions and improve the prediction, we employed a Hopfield neural network, in which the natural limitations on protein tertiary structure and preference of chemically stable long beta-sheet are expressed in a form of energy functions. To clarify the prediction for heads and tails of beta-sheets, special variables are introduced, which are similar to the line process proposed by Geman.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Factual
  • Mathematics
  • Models, Chemical
  • Neural Networks, Computer*
  • Protein Structure, Secondary*
  • Thermodynamics