By Christo Christov (Eds.)
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The integral of the normalized probability distribution p1(u), which is by definition unitary, does not contain any information about the interaction free energy. As expressed by Eq. (30), the proportionality constant between p1(u) and the integrand of Eq. (26) is related to the interaction free energy, which is exactly the quantity we are seeking to compute. 40 GALLICCHIO AND LEVY The p1(u) distribution is nevertheless a useful quantity for the analysis of the relative contributions to the binding free energy.
10), the ligand is considered as not interacting with either the receptor or the solvent, whereas in Eq. (23), the average is over the conformations of the receptor and the ligand while both of these interact with the solvent continuum in absence of the binding partner (note the absence of the binding energy term in the denominator of Eq. (23)). The standard binding free energy can then be written as DGbo ¼ DGto þ DGr þ DGI ; ð25Þ where DGt and DGt have the same meaning as in Eq. (13), and DGI is defined by Eq.
26) is related to the interaction free energy, which is exactly the quantity we are seeking to compute. 40 GALLICCHIO AND LEVY The p1(u) distribution is nevertheless a useful quantity for the analysis of the relative contributions to the binding free energy. Using Eq. (26), we can write Eq. (22) as ð Kb ¼ du k ðu Þ; ð31Þ where, based on Eq. (30), k ðu Þ ¼ Vsite Osite Àbu e p0 ðu Þ V 8p2 ð32Þ can be interpreted as a measure of the contribution of the conformations of the complex with binding energy u to the binding constant.
Computational chemistry methods in structural biology by Christo Christov (Eds.)