Protein secondary structure prediction based on quintuplets

Details Protein secondary structure prediction based on quintuplets Protein secondary structure prediction based on quintuplets

2003-07-16

arxiv.org/abs/physics/0307076v1

Physics

Biological Physics

10 pages with 6 tables

Scientific paper

Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length distribution, and focus on inclusion of short range correlations of residues and of conformation states in the models. Conformation-independent and -dependent amino acid coarse-graining schemes are designed for the models by means of proper mutual information. We compare models of different level of complexity, and establish a practical model with a high prediction accuracy.

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