Flexible structural protein alignment by a sequence of local transformations.

ABSTRACT:

Motivation

Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.

Results

We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from th

SUBMITTER: Rocha J 

PROVIDER: S-EPMC2940242 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature