Hi, I am designing a protein interface of a nanobody with my target antigen.
1000 initial poses were generated by patchdock and 1000 designs were generated per each pose.
After ploting the ddg-rmsd scatter plot, I found all the poses has a characteristic scatter plot like fig. A attached (a narrow RMSD range within ~0.25A, while a majority stays exactly at 0.00A).
The design method is generally: dock -> design interface residue within 10A (x 3 times, with minimize and repack after each round) -> final minimize and repack (x 100 times) -> calculate ddg and rmsd
Since I have also got several "more funnel-like" scatter plots by using the same design method on known nanobody-antigen complex structure (fig. B), I wonder if it is really the problem of my design script or/and the problem of the pose.
I am guessing it is too early to discard the pose from fig. A because somehow it looks like the tip of funnels I have seen in other research of interface design.
Then I want to know, is there a way of sampling a wider range of RMSD of poses by Rosetta Dock? Do you think it helps?
Thank you so much!!!