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.