Dear world,
I am computing surface complementarity of one protein cavity with that of
several ligands, for all of which I have X-ray crystal structures.
I also need to compare the surface complementarities of each of the ligands
to the protein with each other.
Would anyone know of any program that I can use to accomplish this? Or, an
algorithm that I can tweak to do the job? Something that determines how
"parallel" the protein cavity and ligand surfaces are and assign a
non-arbitrary score that I can use to compare across different ligands with
the same (or similar) cavity, maybe? (The cavity does change slightly when
different
ligands bind).
I would greatly appreciate any help or guidance.
Thank you very much,
Regards,
Sangeetha Vedula.
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