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- Chen Luonan
- Department of Electrical Engineering and Electronics, Osaka Sangyo University
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- Wu Ling-Yun
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
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- Wang Ruiqi
- Department of Electrical Engineering and Electronics, Osaka Sangyo University
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- Wang Yong
- Department of Electrical Engineering and Electronics, Osaka Sangyo University
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- Zhang Shihua
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
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- Zhang Xiang-Sun
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
抄録
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 http://zhangroup.aporc.org/bioinfo/samo/.
収録刊行物
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- Ｇｅｎｏｍｅ Ｉｎｆｏｒｍａｔｉｃｓ
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Ｇｅｎｏｍｅ Ｉｎｆｏｒｍａｔｉｃｓ 16 (2), 114-124, 2005
日本バイオインフォマティクス学会
