EVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

ABSTRACT:

Background

Many structural bioinformatics approaches employ sequence profile-based threading techniques. To improve fold recognition rates, homology searching may include artificially evolved amino acid sequences, which were demonstrated to enhance the sensitivity of protein threading in targeting midnight zone templates.

Findings

We describe implementation details of eVolver, an optimization algorithm that evolves protein sequences to stabilize the respective structures by a variety of potentials, which are compatible with those commonly used in protein threading. In a case study focusing on LARG PDZ domain, we show that artificially evolved sequences have quite high capabilities to recognize the correct protein structures using standard sequence profile-based fold recognit

SUBMITTER: Brylinski M 

PROVIDER: S-EPMC3735418 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature