Software:Protein-DNA Modeling Interface
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 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.
- protein_dna<at>flash62.bioc.columbia.edu
