Criteria on the calculation of Irmsd of the protein-protein interface

[Anonymous]

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

[Anonymous]

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.

[Anonymous]

Can we make the Irmsd calculation of RosettaDock identical to CAPPR’s? Is there parameter setting to do that? Thanks

[Anonymous]

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?

[Author]

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