Comparison of protein structures by multi-objective optimization.
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/.
Chen
Luonan
L
Department of Electrical Engineering and Electronics, Osaka Sangyo University, Daito, Osaka 574-8530, Japan. chen@elec.osaka-sandai.ac.jp
Wu
Ling-Yun
LY
Wang
Ruiqi
R
Wang
Yong
Y
Zhang
Shihua
S
Zhang
Xiang-Sun
XS
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D040681:Structural Homology, Protein