we've done calculations on protein-protein binding affinity for sets of
mutations using Amber pmemd TI on GPUs and found (in most cases) very good
accuracy vs experiment:
Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid
Experimental and Computational Approach. Zou, J., Simmerling, C., Raleigh,
D., The Journal of Physical Chemistry B 123 (49), 10394-10402 2019
https://pubs.acs.org/doi/10.1021/acs.jpcb.9b08323
we also have a recent review that discusses accuracy of calculations, with
references to recent examples
Protein storytelling through physics
Emiliano Brini, Carlos Simmerling, Ken Dill
https://science.sciencemag.org/content/370/6520/eaaz3041
On Mon, Mar 22, 2021 at 2:01 PM zz sheng <shengzizhang.gmail.com> wrote:
> Hi All,
>
> I would like to estimate protein mutations on protein-protein interaction
> affinity using thermodynamics integration algorithm in pmemd. Does anyone
> tested the accuracy of the approach and how to setup MD simulations in
> Amber?
>
> Thanks,
>
>
> Best,
>
> Zizhang
>
>
>
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Received on Mon Mar 22 2021 - 13:00:04 PDT
