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