How could we relate the experimental ic50 values of ligand molecules with in-silico binding stability results?
A molecules which have a low IC50 (experimental) having high binding stability (studied by docking and dynamics), and a molecule which have high IC50 (experimental) having low binding stability. Is it ok?
I need further clarifications regarding the relation between IC50 and binding affinity!!
It depends on the mechanism of inhibition and on the quantitative difference between "low" and "high" IC50 values; and on the computational technique. Docking scores, derived from single protein-ligand complexes rather than from their ensembles, are unlikely to correlate with IC50 values, regardless of the docking algorithm. Binding free energies obtained from molecular dynamics simulations coupled with free energy calculation (with solvent taken into account explicitly) have uncertainty limit 1-2 kcal/mol in the best case scenario.
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