Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.

ABSTRACT:

Background

Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking.

Results

We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, 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 al

SUBMITTER: Chen L 

PROVIDER: S-EPMC1574323 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature