Benchmarks for flexible and rigid transcription factor-DNA docking.

ABSTRACT:

Background

Structural insight from transcription factor-DNA (TF-DNA) complexes is of paramount importance to our understanding of the affinity and specificity of TF-DNA interaction, and to the development of structure-based prediction of TF binding sites. Yet the majority of the TF-DNA complexes remain unsolved despite the considerable experimental efforts being made. Computational docking represents a promising alternative to bridge the gap. To facilitate the study of TF-DNA docking, carefully designed benchmarks are needed for performance evaluation and identification of the strengths and weaknesses of docking algorithms.

Results

We constructed two benchmarks for flexible and rigid TF-DNA docking respectively using a unified non-redundant set of 38 test cases. The test cas

SUBMITTER: Kim R 

PROVIDER: S-EPMC3262759 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature