CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

ABSTRACT: Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of simi

SUBMITTER: Terashi G 

PROVIDER: S-EPMC4621035 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature