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Hi Rex,
   The protein I'm working on has a defined substrate-binding cleft. I have a model for the apo form but not the substrate-bound complex. I'd like to dock a peptide fragment of its binding partner potentailly involved in the interaction (~8 residues ) to this cleft. My question is what are some programs people find reliable for making a sensible model of a peptide ligand with the right stereochemistry. As I don't have much experience with peptide docking, I'd really appreciate people sharing their own experience : )
Thanks.

On Mon, Jul 11, 2011 at 11:17 AM, REX PALMER <[log in to unmask]> wrote:
Hi
I'm sure I could help but need more details of the actual project you are undertaking.
 
 
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
From: crystal <[log in to unmask]>Sent: Saturday, 9 July 2011, 2:09
Subject: [ccp4bb] peptide docking

Hi all,
   As I'm a newbie in peptide docking, I was wondering what programs/servers people would suggest for generating the peptide PDB (keeping all the proper stereochemistry)?
Is it possible to extract a file from the PDB database?
All comments will be much appreciated!