Beta-sheet Prediction using Inter-strand Residue Pair Propensities

Minoru. ASOGAWA (

Massively Parallel Systems NEC Laboratory, RWCP
4-1-1, Miyazaki, Miyamaeku, Kawasaki, Kanagawa 216, Japan


Usually two residues of a pair in a beta-sheet separated long distance in a protein sequence. Therefore, to achieve high prediction accuracy for a beta-sheet, it is necessary to consider such inter-strand residue interactions. Since widely used methods for a beta-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 beta-sheet, utilizing residue pair propensities, which are calculated from the statistics of inter-strand 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 beta-sheets with high accuracy.