I have attempted to use the RosettaDock webserver for protein-protein docking. If I recall correctly, the webserver is only capable of doing fixed backbone docking simulations. If you are docking a small peptide with a protein I suspect you want the peptide to be somewhat flexible. Although my results from the RosettaDock webserver were disappointing, the more recently developed PyRosetta (pyrosetta.org) is extremely powerful and is certainly capable of doing what you need. PyRosetta is a Python interface to Rosetta, so it requires some knowledge of Python and you need to have the software installed locally, but you can get it to do lots and lots of useful things by writing relatively short scripts. I have had poor luck using webservers for docking, because I have found that often you need to tweak parameters (weights, restraints, etc.) here and there to get the simulations to give sensible results for a particular set of partners and webservers do not give you enough control of the variables.

Good luck,

Mike



----- Original Message -----
From: "Juergen Bosch" <[log in to unmask]>
To: [log in to unmask]
Sent: Monday, July 11, 2011 6:14:20 PM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] peptide docking

Here are some options: 
http://vina.scripps.edu/ 
http://rosettadock.graylab.jhu.edu/ 


Jürgen 



On Jul 11, 2011, at 8:24 PM, crystal wrote: 


Hi Pius, 
Thanks for the tip. I've never used that utility in PyMol. It'll give it go! 
From the drop-down menu of the Builder tab, it seems like one could specify the secondary structure as well. 
Have you ever tried that option? 
Thanks. 


On Mon, Jul 11, 2011 at 12:43 PM, Pius Padayatti < [log in to unmask] > wrote: 


I am just guessing this what you want. 
a peptide of certain length say 10 aa and need it to be built. 
use pymol Builder utility and choose protein and build your peptide. 
you do not need any density. 
write out the co-ordiantes and use it in autodock for docking. 
pius 





On Mon, Jul 11, 2011 at 12:41 PM, crystal < [log in to unmask] > wrote: 
> 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 < [log in to unmask] > 
> 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 
>> 
>> Ph / Waea +64 3 4797293 
>> Fax / Waeawhakaahua +64 3 4797034 
>> 
>> 
>> 
>> From: CCP4 bulletin board [mailto: [log in to unmask] ] On Behalf Of 
>> crystal 
>> Sent: Saturday, 9 July 2011 1:09 p.m. 
>> 
>> To: [log in to unmask] 
>> 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! 
> 






-- 
Pius S Padayatti,PhD, 
Phone: 216-658-4528 







...................... 
Jürgen Bosch 

Johns Hopkins Bloomberg School of Public Health 

Department of Biochemistry & Molecular Biology 

Johns Hopkins Malaria Research Institute 

615 North Wolfe Street, W8708 

Baltimore, MD 21205 

Phone: +1-410-614-4742 

Lab: +1-410-614-4894 

Fax: +1-410-955-3655 

http://web.mac.com/bosch_lab/ 

-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

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