A simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and …

• Abstract
• Introduction
• Methods
• Results and Discussion
• Conclusions
• Software and data availability
• Supplementary data
• References
• Figures
• Tables

The protein–nucleic acid interaction module is implemented in C++ in the ROSETTA software package (http://www.bakerlab.org). ROSETTA software package is freely available to academic users. We hope to foster further development of computational algorithms for protein–DNA binding specificity predictions by providing all experimental datasets used in this study (including G measurements, PWMs and TF binding sites) as Supplementary Data.

SUPPLEMENTARY DATA 

Supplementary Data are available at NAR Online.

ACKNOWLEDGEMENTS 

The authors would like to thank Jonathan Widom for careful reading of the manuscript and many useful suggestions, and Eldon Emberly for providing experimental binding data for several TFs. A.V.M. would like to acknowledge a fellowship from the Leukemia and Lymphoma Society. J.J.H. is a fellow of the Jane Coffin Childs Memorial Fund for Medical Research. Funding to pay the Open Access publication charges for this article was provided by National Institutes of Health (NIH).

Conflict of interest statement. None declared.