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RosettaDock-4.0 score term

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RosettaDock-4.0 score term

Excuse me, I wonder where I can find detailed interpretations of the score terms of RosettaDock-4.0.

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Wed, 2022-06-29 22:07

The general reference for Rosetta score terms is Alford et al.

That should explain most of the standard scoring terms. If there's a particular entry in the score file that's not covered, feel free to ask about it specifically.

Thu, 2022-06-30 06:52

Thank you very much for your explanation.

I have looked through the paper.

What I am wondering is if those terms with prefixes like fa_XXX or hbond_XXX measure only one aspect of the energy.

If I want to pick up better docking models, should I choose the function that combines all of the terms (e.g., total score)?


Another thing I want to confirm is that the score terms related to CAPRI require a reference model (native model).

I wonder whether the prediction with the lowest energy will be used as a reference.

If so, does that mean those CAPRI-related score terms are dependent on the selection of the reference model?

Thank you in advance.

Sun, 2022-07-03 19:34

You should use the I_sc term to pick models. total_score is dependent on the monomer models as well, so it does not discriminate as well. I_sc is the proxy for binding energy in RosettaDock. If you're running the low resolution mode as well with motif dock score (highly recommended; much better than the default centroid score function), the motif_dock_score column is also a very good discriminant. 

You need to set the native structure to get CAPRI-related metrics because they are comparison metrics. The method doesn't assign a native on its own. Without a native structure specified at the start, it will give either NaN or nonsense values for the Irms, Fnat, CAPRI-type columns.

Tue, 2022-07-05 11:07