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 <rex.pal...@btinternet.com>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 <aac...@gmail.com> > > *To:* CCP4BB@JISCMAIL.AC.UK > *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! > > >
