Dear All, Sorry for the late reply. I wish to compare binding pockets of some homologous proteins, a couple of which have a ligand bound, while the rest don't.
I wish to check if there is any difference in the nature of the cavity in the homologous proteins, e.g. properties like hydrophobicity, electrostatics, etc. But I also wish to determine exactly which residues are surfacing/lining the cavity. Thanks and regards, sreetama ________________________________ From: Francois Berenger <beren...@riken.jp> To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 4 October 2012 12:56 PM Subject: Re: [ccp4bb] residues forming the surface of a cavity On 10/04/2012 04:09 PM, sreetama das wrote: > Dear all, > Is there any CCP4 module/ other software/ web server > which can determine which particular residues form the surface of a > pocket/ binding-site in a protein? Do you mean "residues not far from any ligand atom"? And you know where is the ligand. Or do you mean "residues surfacing a pocket or cavity"? Regards, F.
