I'm learning FlexPepDocking from the following paper:
"Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors"
And I want to see the scripts the anthor used, which is named 'FlexPepDockAbInitio' in 'protocol capture archive'.
What is the "protocol capture archive"?! I've googled but found no useful result..
The paper you refer to is part of the RosettaCon 2010 PLoS collection. Although some of the papers have already been published, the collection itself isn't supposed to "go live" until 2-3 weeks from now.
The protocol capture archive is currently stored in the (not publicly accessible) Rosetta code archive, although once the collection is posted as a whole, the protocol capture archive should be available to all through the PLoS collections website.
Thanks, Rmoretti.And I wrote to the corresponding author for the achives
If you contact the corresponding authors directly, I'm sure they'd send it along. I've brought the post to their attention.
Thanks for you reply and kind help,Smlewis.
I did wrote to the author for the archives....But when I found the "collection project" in "Plos Biology", I think I can get it from the website directly, so I wrote to the author again to cancel my application for the archives.
And then I found the archives are still not available on line(@@,I don't know how to deal with this case..bothering her again? Or hopefully she would see this post and give me a copy of that archives).......
The FlexPepDock ab-initio application will be released as part of Rosetta 3.3, which is expected to be released on September 2011. While the protocol capture may help you get an idea of the protocol usage, it cannot be used with the current Rosetta version, and can currently be accessed only by internal Rosetta users. I can of course send you the protocol capture files, if you like (please send me your contact details, in this case).
Thanks for your kind reply. My email is firstname.lastname@example.org , it will be great if you can send me a copy of the protocol capture files.I hope I can get some ideals about how to analyze the docking results and further improve my docking experiments.
Thanks and best wishes,
Well, I have access to the Rosetta SVN but I can't find the folder "protocol_capture/" mentioned here http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_... either.
It would be great if anyone could point me to the right directory.
By the way, is there any documentation on how to run FlexPepDocking with rosetta_scripts?
In developer SVN, the protocol captures are at "/trunk/RosettaCon2010/protocol_capture". For most of the applications, these are echoed to the demos anyway.
flexpepdock does not appear to be compatible with the scripter. (In any case, it does not have any parse_my_tag functions associated with it, which are necessary for the scripter...)
Thanks for the quick response.
I want to run FlexPepDock ab-initio but not finding any protocol and unable to download rosetta database and the roseta script that will be use in runing the tool, plz guide me
Yuan i am also following the same paper and not find protocol will you help me here?
The FlexPepDock protocol captures discussed above are now located in the Rosetta/demos directory of the weekly releases, under demos/protocol_capture/2010/FlexPepDock_AbInitio/
You may also want to look at demos/public/abinitio_fold_and_dock_of_peptides_using_FlexPepDock/ and demos/public/Refinement_of_protein_peptide_complex_using_FlexPepDock/
The demos directory is available with the rest of of the Rosetta distribution by download from https://www.rosettacommons.org/software/license-and-download