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Updated: Aug 14, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix
Lulu Yu1, Yusen Zhang2, Ivan Gutman3
1School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209, China.
Abstract:
We develop a novel position-feature-based model for protein sequences by employing physicochemical properties of 20 amino acids and the measure of graph energy. The method puts the emphasis on sequence order information and describes local dynamic distributions of sequences, from which one can get a characteristic B-vector. Afterwards, we apply the relative entropy to the sequences representing B-vectors to measure their similarity/dissimilarity. The numerical results obtained in this study show that the proposed methods leads to meaningful results compared with competitors such as Clustal W.
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