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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]>
>
> *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!
>
>
>