Using Relax to asses conformational space

[Anonymous]

Hi all,
I am a new user to Rosetta and i have a question regrading the relax protocol. I have been using it to create decoys for a target protein, however, I get a sense that the configurations that I am getting are too close to the original structure and so I am not getting a good enough sampling of the conformational space. Is there another protocol I can try or maybe a flag to be used inside the relax protocol to get a more rigorous sampling?
Thanks,
Gideon

[Anonymous]

You want to use the Backrub Application to create an ensemble of structures for your target protein.
Check it out here:
http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_backrub.html

There is also a server for it as well from the Kortemme Lab:
http://kortemmelab.ucsf.edu/backrub

Cheers.
-J

[Anonymous]

You may also be able to use ab initio folding to generate a wider ensemble.

[Author]

Posts