Estimating entropy from waterswap

[marawanish]

Hi,
I am asking if there is an auxiliary way to estimate the entropy cost associated with ligand binding from waterswap calculation of absolute binding free energy. I can understand that there is an overestimation of binding free energy we got from waterswap of around 15kcal due to neglecting the effect of entropy but is there is a way to include this effect on the fly with the calculation. For example, can we approximate the number of waters, pocket curvature, etc to get an idea.

Thanks in advance,
Regards,
Marawan

[Christopher Woods]

  Dear Marawan,

Thanks for getting in touch. Yes, in theory you could try to account for entropy during the calculation, but we haven't developed any theory or any code to do this. It would be a very interesting research project. If you have any ideas about how this could be achieved then I would be very happy to act as a sounding board.

  Sorry not to be more help,

  Best wishes,

  Christopher

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Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com