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Hi, Try Autodock from Scripps. It worked beautifully for me. The docked peptide explained why initial attempts at crystalizing the peptide/protein complex failed (because of a crystal contact). The crystal structure subsequently confirmed the calculated structure. My peptide is a 6-mer. J Mol Biol. 2004 Oct 1;342(5):1659-74 J Mol Biol. 2007 Jun 22;369(5):1296-306 -- Huiming Li Date: Mon, 11 Jul 2011 17:18:48 -0700 From: [log in to unmask] Subject: Re: [ccp4bb] peptide docking To: [log in to unmask] 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]> To: [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!