[AMBER] accuracy of FEW free energy calculation

From: Albert <mailmd2011.gmail.com>
Date: Fri, 19 Jun 2015 22:44:15 +0200


I've got some concern on the accuracy of FEW tool for free energy

According to the original FEW paper which published on Journal of Comp.
Chem 2013 (34) 965-973

in Table 2, the correlation factor for this TI calculation results
seems to be poor, it is only R^2=0.25, R^2=0.26 for method 1 and method
2 respectively. I am not convinced that this is a confident methods for
widely use in drug discovery.

More recently, Schrodinger released their FEP Mapper tool which make
ligand free energy circle to improve the accuracy. They published this
technology in J. Am. Chem. Soc., 2015, 137(7), 2695–2703 recently. In
that paper, the showed "perfect" correlation plot between prediction and
experimental data. However, recently I used this "perfect" tool coupled
with so called OPLS-2.1 FF to predict my system. After 1 months running
on a powerful GPU workstation for 12 testing candidates, I only got
R^2=0.16 !!! Interestingly, with exactly the same system and starting
structure, I run MM/PBSA which was done in 3 days and it gave me
R^2=0.79 !!!

Now I am really curious about nowadays so called popular methods and
their accuracy.

Does anybody did any benchmark of FEW in Amber?

I would be very interested in to see the results.



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Received on Fri Jun 19 2015 - 14:00:02 PDT
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