Hello everyone,
I wrote a script to perform RosettaDesign (both fixbb and flxbb) and I benchmarked it. Attached is the Abinitio folding simulation of three proteins, and my full script can be found here: https://github.com/sarisabban/RosettaDesign/blob/master/RosettaDesign.py
Even though the RosettaDesign computation completes without any errors and I get nice new designed structures, when I evaluate their folding using Abinitio I get very bad results, none of them generates a funnel plot (except for the first protein - but then again the original non-designed structure also forms a funnel anyway, so there is no difference nor improvement)
My question is:
- Evaluating a RosettaDesigned structure using Abinitio is correct, right?
- How can I improve my RosettaDesign protocol to take a protein’s structure and design it to give me a funnel shaped Abinitio plot result? What can I improve?
- Are there things I should do before/after the RosettaDesign? use additional movers?
Your help would be greatly appriciated.
Attachment | Size |
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Abinitio Results | 486.1 KB |
Category:
Post Situation:
First, you're absolutely correct that "forward folding" (running designs through abinito runs) is a good way to validate your designs. In fact, it's the primary method the Baker lab uses to validate their small monomer designs.
Not getting funnel plot on designs is somewhat expected. Chances are that many of your designs aren't going to work. Even if everything is going well, a fair number of raw designs fail forward folding. Depending on how many designs you've forward folded, you may just have too few. You're probably going to need to forward fold thousands of designs to get a handful which pass.
There are certainly tricks which you can use to increast the likelihood that a design going into forward folding is going to give a decent result. I highly recommend a close reading of the Baker lab design papers to see what techniques they applied in their cases.
The major one which immediately comes to mind is fragment quality screen. A protein is only going to forward fold if you get decent fragments. What you can do is run fragment prediction on your designs, then check to see what the lowest rmsd is for the fragments to the "desired" backbone structure. Generally speaking, you want a low rmsd, particularly in the helicies and sheets. You can sometimes get away with some poor fragments, but if you have stretches of the protein all giving you bad fragments, then it's unlikely forward folding will work.
People have played around with puting this sort of information in the actual design process itself (so during the design runs incorporating a fragment quality score as part of the design score), but I'm not familiar enough with the details to know how best to do this. (Again, take a look at the Baker lab papers and see what they do.)