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PubMed · 16901095

Comparison of protein structures by multi-objective optimization.

Luonan Chen·Ling-Yun Wu·Ruiqi Wang·Yong Wang·Shihua Zhang·Xiang-Sun Zhang
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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/.

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AlgorithmsComputational BiologySequence AlignmentStructural Homology, ProteinComparative StudyJournal Article

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Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shihua Zhang, Xiang-Sun Zhang. 2005. Comparison of protein structures by multi-objective optimization.. https://pubmed.ncbi.nlm.nih.gov/16901095/

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