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Updated: Jun 21, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A simple method of identifying symmetric substructures of proteins
Hanlin Chen1, Yanzhao Huang, Yi Xiao
1Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Abstract:
Accurate identifications of internal symmetric substructures of proteins are needed in protein evolution study and protein design. To overcome the difficulties met by previous methods, here we propose a simple quantitative one by using a similarity matrix plus Pearson's correlation analysis. The distance root-mean-square deviation (dRMSD) is used to measure the similarity of two substructures in a protein. We applied this method to the proteins of the beta-propeller, jelly roll, and beta-trefoil families and the results show that this method cannot only detect the internal repetitive structures in proteins effectively, but also can identify their locations easily.
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