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computing Pnear for Rosetta ligand docking

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computing Pnear for Rosetta ligand docking


I am calculating the Pnear for the Rosetta ligand docking outputs to evaluate the funnel-likeness of energy vs RMSD by treating the lowest energy model as the native structure. Is it right to use binding energy and ligand RMSD (no superposition) as E and RMSD in Pnear formula? I see in the papers it is used for de novo designs and they use the total energy and general RMSD.

I really appreciate your help.

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Mon, 2021-02-01 08:27

Yes, that's reasonable.

PNear is simply a calculation of the "funnelness" of the score-vs-rmsd plot. For protein folding you typically evaluate the total score vs. rmsd plot, whereas with ligand docking you use the binding energy vs. ligand RMSD plot. The "funnelness" of the plot would be calculated similarly.

The only potential consideration is that you may or may not need to adjust some of the adjustable parameters in the PNear calculation. The scale of the plot (both energy difference and rmsd) are slightly different from protein folding plots versus the ligand docking plots, and as such the adjustable parameters might need to change to better match. -- It's probably close enough that it really doesn't matter. (I haven't bothered when I've done PNear with ligands.) But if you're not getting the discrimination you want in ranking the quality of the funnel plots, it's something to potentially consider.

Tue, 2021-02-09 09:37