Thank you very much for your insightful suggestions.currently , i am generating 10000 structures. How much rmsd cut off you suggest is good for clustering and how do i proceed to improve the predicted structures. I don’t have any slightest idea how my structure look like, as you suggested inducing point mutations is very good idea, unfortunately, my work is only insilico. so are there any ways of computational structural validation .
Finally, i am curious to know, when you are going to release rosetta3.2 ( looking for flexipepdock module)
your suggestions will greatly help my research