[gmx-users] binding_affinity

[Justin A. Lemkul]

shahid nayeem wrote:
> Dear All
> I have some protein complex pdb after docking two monomers. The
> scoring of these docked structure are not true representative of
> binding affinity. I want calculate the binding affinity affinity of
> these docked pdb. Can anyone suggest me, how should I proceed.
> Shahid Nayeem

Calculating a PMF is a common approach.

http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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