Software:Protein-DNA Modeling Interface General Description

From Honiglab_public

The program interface model (intf_model.exe) can be used predict the conformation of the sidechains within a protein-DNA binding interface as described in Siggers & Honig (2006) (submitted). 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.