Hi all,
Thanks for all the helpful suggestions. It seems like Phenix LigandFit
requires density for the ligand but unfortunately I only have the
ligand-free model. I've tried blasting the peptide sequence using the
"sequence search" tool in the PDB but failed to get any hits. I was
wondering how one could "grep it out of a set of PDB files like Robbie has
mentioned. Since there is relatively high conformational flexibility, I was
thinking about starting with a 5-mer. Does that sound reasonable with people
who have experience with peptide docking? Pius mentioned about making the
model in Coot, PyMol etc. Do you need density in order to fit the ligand or
can one just mutate residues along a strand in an existing model to the
desired sequence and use that fragment for docking?
Thanks for the helpful feedback, everyone.
On Sun, Jul 10, 2011 at 8:54 PM, Joel Tyndall <joel.tynd...@otago.ac.nz>wrote:
> How big is the peptide?****
>
> ** **
>
> _________________________________****
>
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand ****
>
> Skype: jtyndall
> http://www.researcherid.com/rid/C-2803-2008****
>
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
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> Ph / Waea +64 3 4797293
> Fax / Waeawhakaahua +64 3 4797034****
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> ** **
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
> crystal
> *Sent:* Saturday, 9 July 2011 1:09 p.m.
>
> *To:* CCP4BB@JISCMAIL.AC.UK
> *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!****
>
