some Q/A about SnugDock

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        ! some Q/A about SnugDock

        ref: [|SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models]

        Q: questions from Jarod ; A: answers from Aroop Sircar and Jeffrey J. Gray .

        Thanks for the quick replies from Aroop and Jeffrey.

        -=Q/A 1=-

        __Q__: As you mentioned in the paper, you rank the docking decoys by the
        interface energy scores rather than the total score, how could I read
        the interface energy from the score file “aaFR02.fasc”?

        __A__: The column header for interface score is “I_sc”

        -=Q/A 2=-
        __Q__: In the first paragraph of section ‘Global docking’, it said “The
        starting structures consisted of the unbound crystal structure of the
        antigen and the lowest-interface-energy RosettaAntibody homology
        model.”; But in the other parts of this paper, the
        starting structures of antibodies are “lowest-energy RosettaAntibody
        homology model” rather than “lowest-interface-energy” ones, and I
        don’t find the column header “I_sc” in the score file generated by

        __A__: It should read lowest-scoring instead of lowest-interface-scoring.

        -=Q/A 3=-
        __Q__: can Ensemble+SnugDock run in centroid mode for global docking?

        __A__: SnugDock is only applicable in full atom (high-resolution) mode.

        -=Q/A 4=-
        __Q__: Have you tested the SnugDock for the complex where the antigen is
        very small like a peptide? how do you treat the water molecules during docking?

        __A__: We have not benchmarked against peptide targets because, as you note, they have some different physics such as flexibility and more importance for water-mediated hydrogen bonds. Rosetta does not have any tested means for including explicit waters. For peptide docking, I’d refer you to a paper on HIV-protease by Sid Chaudhury in my lab, and a new paper by Ora Furman’s lab on peptide docking with Rosetta.

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