Comparison of Protein Structures by Multi-Objective Optimization

Luonan Chen[1] (
Ling-Yun Wu[2] (
Ruiqi Wang[1] (
Yong Wang[1] (
Shihua Zhang[2] (
Xiang-Sun Zhang[2] (

[1]Department of Electrical Engineering and Electronics, Osaka Sangyo University, Daito, Osaka 574-8530, Japan
[2]Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China


We propose a novel method for solving the structure comparison problem for proteins, based on a decomposition technique. We define the structure alignment as a multi-objective optimization problem with both discrete and continuous variables, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. The software is available upon request, or from

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Japanese Society for Bioinformatics