jwohlwend
Meaning of affinity_pred_value
The documentation states that "It reports a binding affinity value as log(IC50), derived from an IC50 measured in μM". This implies that tighter binders (lower uM values) would have lower values of affinity_pred_value.
However, when I ran many proteins against the same ligand, I found a fairly strong positive correlation between affinity_probability_binary and affinity_pred_value (Spearman rho ~= 0.5).
Probably the documentation is just wrong and a higher affinity value corresponds to tighter binding? Please clarify, thanks.
Hi @morgannprice , no the documentation is correct, but the affinity_pred_value should only be used when comparing different binders (e.g. in a hit / lead optimization setting) not when comparing different hit from decoys. So in your setting, I would use affinity_pred_value if trying to understand selectivity of a particular binder to similar proteins, affinity_probability_binary if trying to screen a ligand against many different proteins to see which could bind to it.
