Hi to all!

I have read about the client update. I noticed that includes the support for symmetry in the hybrid protocol for comparative modeling.

Can I ask more information about this new function?

Thanks in advance for any replies.

Bye!!!

Hi Andrea,

I am one of the Rosetta developers who has been developing the hybridization protocol.

Most of the recent updates on the Rosetta@home project have been in preparation for the upcoming CASP10 structure prediction competition. In particular, we have been developing a new "hybridization" protocol for comparative modeling. The basic idea of comparative modeling is that, if we want to determine the structure of some protein, it is likely to be similar to the structure of proteins with similar amino acid sequences (known as "template" structures). With so many protein structures already solved, given some protein of interest, it is often the case that there are several proteins with similar sequence whose structure is already known.

Previously, when more than one template structure is known, Rosetta could only sample protein conformations using one template at a time. The new hybridization protocol is exciting because it allows us to simultaneously sample features from different templates. This often leads to improved accuracy in structure prediction, as we can sample the most accurate features from many different templates.

The most recent update (3.24) adds symmetry support to hybridization. Some protein structures exist in nature not alone, but in a larger complex containing 2 or 3 (or more) identical copies. In order to accurately predict the structure of these proteins, we must take into account the conformations of these identical copies. With the latest BOINC code, we may borrow no just the structure from template structures, but also the oligomeric assembly, that is, the way in which the identical subunits are assembled.

I'm more than happy to answer any questions about this protocol (or about CASP10).

-Frank

Hi Frank, thanks for the reply!

So now are you testing if this new protocol can give better results or at least faster than the previous one?

Thanks in advance! And sorry for my poor english!

Bye!