β-sheet Prediction using Inter-strand Residue Pair Propensities

Abstract

Usually two residues of a pair in a β-sheet separated long distance in a protein sequence. Therefore, to achieve high prediction accuracy for a β-sheet, it is necessary to consider such inter-strand residue interactions. Since widely used methods for a β-sheet prediction are only based on subsequence of residues, generally 20 residues, they cannot achieve high prediction. In this paper, we describe a novel method to predict an anti-parallel and parallel β-sheet, utilizing residue pair propensities, which are calculated from the statistics of interstrand residue pairs. With primary experiment, it is shown that residue pair propensities are consistent with the result of real protein experiment and can detect parallel β-sheets with high accuracy.