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Joined: 12/10/2008
Groups: None

Hi everyone,

I've tried looking for the answer, and maybe I just haven't found the right references, but what is the algorithm that foldIt uses for the backbone wiggling procedure? Is it based on rotamers? Is there a reference I could look up? I just found it pretty neat and I'm wondering how the little perturbations are done. I'm assuming the sidechain wiggling is rotamer based with clash considerations in the picture? Seeing it happen 'live' is neat. Is it Rosetta functions running behind the scenes that handles this, or something else?

Thanks!

Joined: 05/09/2008
Groups: None
Yes, Rosetta functions is correct.

From the recent Nature paper (http://www.nature.com/nature/journal/v466/n7307/full/nature09304.html):

"Available automatic moves—combinatorial side-chain rotamer packing (‘shake’), gradient-based
minimization (‘wiggle’), fragment insertion (‘rebuild’)—are Rosetta
optimizationsmodified to suit direct protein interaction and simplified
to run at interactive speeds."

If you have more detailed questions there is a new thread for this:
http://fold.it/portal/node/988695

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