SurfaceMatch is a simple pair of programs for trying to match two surfaces for guiding docking. It was written while self-employed and visiting DKfz.
surface takes a PDB file and generates a list of surface features.
Optionally it can take a file containing residue ranges to restrict
the analysis to part of the protein surface.
match takes two output files from surface. The first is a pattern
from one structure which is searched across the pattern of the second
structure. The first pattern will be smaller than the second. For
example, the first might be a peptide or ligand being searched against
a protein. Alternatively, the first might be likely contact residues
in the CDRs of an antibody being searched against an antigen.
You must install BiopLib (http://www.bioinf.org.uk/software/bioplib)
and can then simply run the compile.sh script.