DNA-Binding Domain Hunter (DBD-Hunter) is a knowledge-based method for predicting DNA-binding proteins function from protein structure. The method combines structural comparison and evaluation of DNA-protein interaction energy, which is calculated use a statistical pair potential derived from crystal structures of DNA-protein complexes. Details of the method is described in the reference below.

To use the webservice of this program, please upload a protein structure file in the PDB format. The results will be sent back to your through e-mail address you provided. Alternatively, DBD-Hunter may be accessed from may be accessed from PSiFR.


  • This service is freely available to academic users and not-for-profit institutions.
  • Commercial users may request an evaluation copy from skolnick@gatech.edu .
  • Commercial users may license the DBD-Hunter software after completing the license agreement and sending it to skolnick@gatech.edu . Download the license agreement.

If you find the service useful, please cite the following publication:

M. Gao and J. Skolnick. 2008. DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Research, 36(12): 3978-3992. PDF Supplementary

Submit Your Structure Here

Structure must be in the PDB format. Field marked with (*) are required.

Structure name

Upload structure*

Your Email Address*

Benchmark Datasets

  • DB179 (DNA-binding proteins)
  • NB3797 (Non-DNA-binding proteins)
  • APO-HOLO 104 (DNA-binding proteins in DNA-free and DNA-bound forms)
  • SG1697 (Structural genomics targets)

Statistical Pair Potential

This page is maintained by Mu Gao.