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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Fri Apr 23, 2010 9:23 am 
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I'm going to verify the accuracy of AutoDock Vina by using PDBbind as the testing data. The output of Vina is the free energy in kcal/mol. However, the affinity in PDBbind is pKd or pKi. I don't know how to relate free energy in kcal/mol and affinity in pKd? In the 2002 XScore paper, I find a sentence saying that pKd units "can be converted into binding free energies at 298K in kcal/mol by multiplying a factor of -1.36." I'm wondering how the factor of -1.36 originates? I find the equation deltaG = -RTlnKd, but don't know how to make use of it. Besides, I used 1HXB of PDBbind as a test case. The affinity retrieved from PDBbind is Ki=0.12nM, or pKi = 9.92. Multiplying pKi by -1.36 yields 9.92*(-1.36) = -13.49, but the lowest free energy of the docking result of 1HXB is -10.8 kcal/mol. Therefore I'm not sure how to correctly use PDBbind as testing dataset to re-verify the correctness of Vina.

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