RMSD AND CONSENSUS STRUCTURE
Hi, I'm trying to do an RMSD analysis between a series of target proteins and a protein family to select the most unusual among them. I was thinking of getting a consensus on the structure of the family in question and then do the RMSD of the target proteins against the common structure of the family. How could I do that? thanks in advance for the help.
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danilobritorocha •
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Another way: we have six proteins; P1, P2, P3, P4, P5 and P6. How do I calculated the RMSD of P1 against the anothers five proteins in a correctly manner? Just get the average RSMD? this do not seems right to me...
Have you thought of the following - perform an all vs all RMSD (P1 vs P2, P1 vs P3, ... P4 vs P5). If there indeed is an outlier then you should have all the pairs that has that protein (ex - P3) will have larger RMSD, whereas all the other pairs that do not have P3 will have low RMSD