Protein fold recognition based upon the amino acid occurrence

Authors:
Y.-H. Taguchi;M. Michael Gromiha
Affiliations:
Department of Physics, Chuo University, Tokyo, Japan;Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
Venue:
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
Year:
2007

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Abstract

We have investigated the relative performance of amino acid occurrence and other features, such as predicted secondary structure, hydrophobicity, normalized van der Waals volume, polarity, polarizability, and real/predicted contact information of residues, for recognizing protein folds. We observed that the improvement over other features is only marginal compared with amino acid occurrence. This is because amino acid occurrence, indirectly, can consider varieties of physical properties which are useful to discriminate protein folds. If we consider only proteins which are well aligned structurally with each other, the accuracy of discrimination is drastically improved. In order to discriminate protein folds more accurately, we need to consider anything other than structure alignment.