Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.

ABSTRACT: The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long been challenges that prevented the development of efficient protein-DNA docking methods. We have demonstrated the ability our flexible data-driven docking method HADDOCK to deal with these before, by using custom-built DNA structural models. Here we put our method to the test on a set of 47 complexes from the protein-DNA docking benchmark. We show that HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s). Our DNA analysis and modelling procedure captures the bend and twist motions occurring upon complex formation and uses these to generate custom-built DNA structural models, more closely resembling the bound form, for use in a seco

SUBMITTER: van Dijk M 

PROVIDER: S-EPMC2943626 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature