Hi guys,
First of all: I'm completely new to the whole protein structure and prediction so please be not too harsh on me^^
I'm interested in the structural differences of different patient-derived mutant forms of a protein of interest. I predicted the structure of my protein of interest (USH1G) as well as a mutant form (S243E) with Robetta.
However when I try to align those to PDB structures via PyMOL with the command "align prot1, prot2" the RMS value is 14.578. This seems to be rather strange since the sequence is completely similar except for the amino acid 243.
Can somebody explain this phenomenon to me or tell me what I'm doing wrong?
Thank you.
How many models have you generated through Robetta? Because these two are alike, but not that much. If you use the command cealign instead of align, you get a better result, however, it should be better.
I would recommend you try AlphaFold and see if you get similar results for both proteins.
Hi Lorenzo, thank you for the quick answer I will try your suggestions.
I believe it's a limitation of the predictive algorithms. I've done the same with I-Tasser and gotten the same thing. There's STRUM, it predicts the fold stability of single protein mutations, however it's currently down.