Software:Protein-DNA Interface Alignment Software General Description
From Honiglab_public
Introduction:
The protein-DNA alignment software allows one to align the interfacial amino acids from two protein-DNA complexes based on the geometric relationship of each amino acid to its local DNA. The algorithm is described in detail in the paper Siggers et al. Structural Alignment of Protein-DNA Interfaces: Insights inot the Determinants of Binding Specificity. JMB 345(5):1027-45 (2004). The programs described here allow the user to take two PDB files that both contain protein-DNA complexes and to perform an interface alignment of the two complexes. The programs will output the aligned residues and their corresponding residue-residue similarity scores, s(i,j). The alignment program will also report the interface alignment score (IAS) which provides a measure of the similarity of the docking geometry for the two proteins onto their DNA substrates.
Protein-DNA Interface Alignment Software is supported by a funding from the National Science Foundation Grant # DBI-9904841
Developed in the Honig Lab
