I was designing the "interface" (possible contacts) of a fusion protein using FastDesign. Since I was running the appliction on a laptop, so far only 200 designed models have been genrated.
I then went on to analyze the result anyway and tried to plot Score VS caRMSD (as shown in the attached file). Here are my questions:
(1) When plotting Score VS caRMSD, i chose the decoy with the lowest total score as the reference to calculate RMSD against. Is this reasonable? if not, what structure should i choose as the referece? The fusion protein model before design is generated by FastRelax and i don't think it's a "native" structure.
(2) Dose the current Score VS caRMSD plot look good or show some degree of convergence? Or i have to generate more decoys so that i can tell the degree of convergence? And how many decoys should be generated? I heared from some authors that they sometimes only generate one designed sequence and just go on without extensive design.
(3) This may sound naive but i am wondering when i choose the model with lowest score as the referecen and plot the Score VS RMSD, which structure should i choose as the best one? Isn't the reference decoy the best one?
Thank you very much