Re: Protein-ligand affinity

From: Kenno Vanommeslaeghe (
Date: Tue Oct 15 2013 - 14:40:50 CDT

On 10/15/2013 01:42 PM, James Starlight wrote:
> Also I've found that Free energy perturbation and Thermodynamic
> integration could be usefull for affinity measurements.

They're the gold standard, but that comes at a cost. Be advised that FEP
and TI are often a bit less trivial to set up than other types of
calculations, and are computationally expensive. Moreover, special
precautions may need to be taken when studying a buried site. It *might*
be easier to start with something like MM/PBSA, as Aaron suggested
(provided that the buried site is handled correctly).

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