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Open Access Methodology article

Protein-DNA docking with a coarse-grained force field

Piotr Setny1*, Ranjit Prasad Bahadur2 and Martin Zacharias1

Author Affiliations

1 Physics Department T38, Technical University Munich, James Franck Str. 1, 85748 Garching, Germany

2 Indian Institute of Technology Kharagpur, Kharagpur - 721302, India

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BMC Bioinformatics 2012, 13:228  doi:10.1186/1471-2105-13-228

Published: 11 September 2012

Abstract

Background

Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming an increasingly important tool in the field of macromolecular assemblies, complementing particularly demanding protein-nucleic acids X ray crystallography and providing means for the refinement and integration of low resolution data coming from rapidly advancing methods such as cryoelectron microscopy.

Results

We present a new coarse-grained force field suitable for protein-DNA docking. The force field is an extension of previously developed parameter sets for protein-RNA and protein-protein interactions. The docking is based on potential energy minimization in translational and orientational degrees of freedom of the binding partners. It allows for fast and efficient systematic search for native-like complex geometry without any prior knowledge regarding binding site location.

Conclusions

We find that the force field gives very good results for bound docking. The quality of predictions in the case of unbound docking varies, depending on the level of structural deviation from bound geometries. We analyze the role of specific protein-DNA interactions on force field performance, both with respect to complex structure prediction, and the reproduction of experimental binding affinities. We find that such direct, specific interactions only partially contribute to protein-DNA recognition, indicating an important role of shape complementarity and sequence-dependent DNA internal energy, in line with the concept of indirect protein-DNA readout mechanism.