Re: [ccp4bb] Shape similarity of ligand binding sites

Hi Stephen, I have a python script that does exactly that. It uses a surface calculated by MSMS and calculates the similarity using a function like that of the SC program. You'll need to align the structures first. There is an equivalent script that calculates the complementarity of two

Re: [ccp4bb] Shape similarity of ligand binding sites

Hi Steve, Have you tried CASTp server (http://sts.bioe.uic.edu/castp/). That should help you to compare the shape of the ligand-binding sites. Best wishes, Avinash

Re: [ccp4bb] Shape similarity of ligand binding sites

Hi Stephen, I've had some luck calculating ligand-binding cavity volume with the 3v website (http://3vee.molmovdb.org/). You might want to give it a shot. Best, Chris On Wed, Jun 14, 2017 at 12:42 PM, < stephen.c...@rc-harwell.ac.uk> wrote: > Dear ccp4bb, > > I am trying to compare the shape

[ccp4bb] Shape similarity of ligand binding sites

Dear ccp4bb, I am trying to compare the shape of a ligand binding site in my protein with that of some homologues and mutants and was wondering how others go about this? I specifically want to compare the shapes of the surface (similar to an sc analysis of an interface) rather than the