Autodock Vina calculates "binding affinity" in kcal/mole. Is it somehow connected to activation energy in Arrhenius equation?
I am thinking about this equation (for non diffusion limited binding):
Ea = -RTln(kon/kdiff)
where kon is the forward rate of binding (M/s)
and kdiff is for diffusion limited binding
further explanation about formula may be found in Jones, M. V, Sahara, Y., Dzubay, J. a, & Westbrook, G. L. (1998). Defining affinity with the GABAA receptor. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 18(21), 8590–8604.
Taking kon from experimental studies (or presented paper) gives Ea ~ 4 kcal/mole . My calculation in Autodock Vina are resulting in binding affinity of -5 kcal/mole . So, the abosolute value is within method error, what is mysterious for me is a negative value (or positive value calculated in Arrhenius formula). The question is wether negative value is due to some convention in Autodock calculations and may be applied as activation energy? And in more general - what is autodock vina "binding affinity" in terms of physical chemistry?
In more conventional terms "binding affinity" = deltaG = RTlog(Kd), where G is Gibbs free energy, Kd = kon/koff is equilibrium dissociation constant. Do not expect a significant correlation between deltaG and a scoring function (either Vina's or any other one). The intended use of scoring functions is not calculating binding affinities for individual molecues, but rather "enriching" large data sets in active compounds.
If you calculate energy of binding EA from experimental data, you should get negative value as the binding process releases energy. That means Vina is right and in your calculation is mistake.
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