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

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    • February 21, 2012 at 3:06 pm #1167
      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

      • February 21, 2012 at 3:31 pm #6670
        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.

        • February 23, 2012 at 12:13 am #6677
          Anonymous

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

          • February 26, 2012 at 6:03 pm #6696
            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?

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