This site provides a means of determining if a 3D protein target is a DNA-binding protein with a Helix-Turn-Helix (HTH) structural motif.
This is based on determining if:

• the protein matches with a set of 3D structural templates of motifs that are known to bind DNA,
• if the matched region is sufficiently accessible,
• if the matched region has a sufficiently positive electrostatic potential in its neighbourhood.
  

While other DNA-binding motifs exist (Helix-loop-Helix, Helix-Hairpin-Helix), a simple HMM search is probably more efficient in their case.

Select PDB file to be uploaded:

Select a single PDB protein chain from this file
If there is no chain id enter 0 (zero).

The methods upon which the above observables are generated are described in the paper

Identifying DNA binding proteins using structural motifs and the electrostatic potential
H.P. Shanahan, M.A. Garcia, S. Jones & J.M. Thornton (2004)
Submitted for publication in Nucleic Acids Research

Details of how these observables are implemented will be found in
PDNA-pred : a DNA-binding protein detector
H.P. Shanahan, C. Ferrer, S. Jones, S. Teichmann & J.M. Thornton (2004)
in preparation

Until then, please feel free to contact us.