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" <[email protected]> To: [email protected] 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 < [email protected] > 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 < [email protected] > 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 < [email protected] > > 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: [email protected] ] On Behalf Of >> crystal >> Sent: Saturday, 9 July 2011 1:09 p.m. >> >> To: [email protected] >> 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 [email protected]
