I noticed that in the paper (Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., Gray, J. J.; (2011) Benchmarking and analysis of protein docking performance in RosettaDock v3.2. PLoSONE), the one of the evaluation criteria of docking performance, I_rmsd is defined differently from the CAPRI.
It is:
The interface is defined as all residues with an intermolecular distance of at most 4.0 A.
The CAPRI definition is:
the interface residues in the target were redefined as those having at least one atom within 10 A of an atom on the other molecule.
But in that paper, it states that it takes the same definition as CAPRI. So I have a question, is the calculation of I_rmsd implemented in the RosettaDock the same as the CAPRI?
Thanks for considerations
I looked back at the reference, and you are correct - our I_rmsd metric is different from the CAPRI metric.
The PlosOne paper does correctly state how we calculated I_rmsd, but it incorrectly states that it is identical to CAPRI's. That is an error in the manuscript - sorry.
Can we make the Irmsd calculation of RosettaDock identical to CAPPR's? Is there parameter setting to do that? Thanks
Not without going in and modifying the code.
From my own memory, the CAPRI settings have varied over the years - it may be that it matched the criteria in one CAPRI but not another?