intf_model (The program interface model) can be used predict the conformation of the sidechains within a protein-DNA binding interface as described in Siggers and Honig, (2007) Nucl. Acid Res. 35:1085-1097.. The program allows the identity of the amino acid and base residues in the interface to be changed by the user. Generating multiple, modeled protein-DNA complexes by modeling the binding interface of a protein-DNA complex with multiple DNA sequences, followed by a binding energy calculation on the modeled complexes, provides a way to predict the binding specificity of a protein for different DNA sequences.
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Siggers & Honig (2007)
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry
Nucl. Acid Res. 35:1085-1097