Re: [AMBER] Protein-protein binding free energy MMPBSA

From: David A Case <>
Date: Thu, 14 Oct 2021 21:26:58 -0400

On Thu, Oct 14, 2021, Rana Rehan Khalid wrote:
>I used to calculate the binding free energy of different single
>position mutants protein-protein complexes.

You don't say if (or how) you computed the entropy change upon binding one
protein to a second protein, but this would be a big component of the total
free energy of binding.

>But the results are not comparable with the experimental energies.

You also don't say what "not comparable" means.

If you have a series of point mutants, you might try the assumption that the
entropy loss upon binding is the same for all of the mutants. Then that
term would cancel in calculating delta-delta-G, i.e. in looking at the
difference between two mutants, rather than the absolute binding energy for
any one of them.


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Received on Thu Oct 14 2021 - 18:30:03 PDT
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