CABS is able to conduct blind docking of peptides. You may also use the predicted poses as starting structures for the Rosetta. Have a look at this:
http://www.springerlink.com/content/p6223376886054m6/ On 12 April 2011 10:22, Thomas Evangelidis <teva...@gmail.com> wrote: > I suppose by "full body dock" you mean rigid body docking, correct me if I > am wrong. In that case you could create initial starting structure for > flexible peptide docking. Rosetta accepts even coarse-grained models, namely > only the backbone, and then builds the full-atom structures. > > Alternatively you could predict potential peptide binding sites on your > protein (i.e. by using this server > http://pepsite.russelllab.org/index.html) and the run SMD to force the > peptide to attach to these putative binding sites, and thus create initial > coordinates for Rosetta. This approach is more tedious. Nevertheless, > flexible peptide docking with Rosetta takes approximately 3 minutes per > decoy on an average node and has sub-angstrom accuracy. Posting a question > in the Rosetta forum doesn't sound like a bad idea. > > > On 12 April 2011 03:11, bharat gupta <bharat.85.m...@gmail.com> wrote: > >> but using docking I have to fix the grid and have to dock at that >> position... which is not my objective ... I want the peptide to come and >> bind own its own to the protein... I have heard of full body dock , in which >> there is no need to define grid points , will that be useful ?? >> >> >> On Mon, Apr 11, 2011 at 2:02 PM, Thomas Evangelidis <teva...@gmail.com>wrote: >> >>> You can try Rosetta for flexible peptide docking. >>> >>> >>> >>> On 11 April 2011 15:32, Mark Abraham <mark.abra...@anu.edu.au> wrote: >>> >>>> Hi, >>>>> >>>>> I want to know how can I predict where a designed peptide will bind to >>>>> my protein target or not using simulation ... Can anybody guide me ?? >>>>> >>>> >>>> I don't think anybody has the computational resources to answer this >>>> question with unguided MD. Docking programs are probably the way to get a >>>> guide about what binding modes might be reasonable, but I don't know what >>>> software might be fit for the purpose. >>>> >>>> Mark >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> >>> -- >>> >>> ====================================================================== >>> >>> Thomas Evangelidis >>> >>> PhD student >>> >>> Biomedical Research Foundation, Academy of Athens >>> >>> 4 Soranou Ephessiou , 115 27 Athens, Greece >>> >>> email: tev...@bioacademy.gr >>> >>> teva...@gmail.com >>> >>> >>> website: https://sites.google.com/site/thomasevangelidishomepage/ >>> >>> >>> >>> >>> -- >>> >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com >> >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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