SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment.

ABSTRACT: Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights into protein functional similarities. Existing structure alignment tools adopt a two-stage approach to structure alignment by decoupling and iterating between the assignment evaluation and structure superposition problems. We introduce a novel approach, SAS-Pro, which addresses the assignment evaluation and structure superposition simultaneously by formulating the alignment problem as a single bilevel optimization problem. The new formulation does not require the sequentiality

SUBMITTER: Shah SB 

PROVIDER: S-EPMC3360771 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature