Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.

ABSTRACT:

Background

Protein fold recognition usually relies on a statistical model of each fold; each model is constructed from an ensemble of natural sequences belonging to that fold. A complementary strategy may be to employ sequence ensembles produced by computational protein design. Designed sequences can be more diverse than natural sequences, possibly avoiding some limitations of experimental databases.

Methodology/principal findings

WE EXPLORE THIS STRATEGY FOR FOUR SCOP FAMILIES: Small Kunitz-type inhibitors (SKIs), Interleukin-8 chemokines, PDZ domains, and large Caspase catalytic subunits, represented by 43 structures. An automated procedure is used to redesign the 43 proteins. We use the experimental backbones as fixed templates in the folded state and a molecular mechanic

SUBMITTER: Schmidt Am Busch M 

PROVIDER: S-EPMC2864755 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature