High performance transcription factor-DNA docking with GPU computing.

ABSTRACT:

Background

Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. More importantly, experiments show that the docking quality depends on the coverage of the conformational sampling space. It is therefore desirable to accelerate the computation of the docking algorithm, not only to reduce computing time, but also to improve docking quality.

Methods

In an attempt to accelerate the sampling process and to improve the docking performance, we

SUBMITTER: Wu J 

PROVIDER: S-EPMC3380734 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature