Docking Score Interpretation

The numerical docking score generated by a docking calculation provides a relative, rather than absolute, estimate of predicted binding affinity, and should...

The numerical docking score generated by a docking calculation provides a relative, rather than absolute, estimate of predicted binding affinity, and should always be interpreted comparatively — ranking candidate compounds against one another and against a known active reference compound docked using the identical protocol — rather than as a standalone, quantitatively precise prediction of true binding free energy. A more negative (or, depending on software convention, more positive) score indicates a more favourable predicted interaction, but because absolute docking scores are not reliably transferable between different targets or different docking programs, meaningful interpretation requires a consistent internal benchmark, most commonly the docking score obtained for a well-characterised reference ligand against the same target using the identical protocol.