Docking Score vs Binding Affinity: What Researchers Should Actually Report

By BioDockify Computational Research Team · August 8, 2026 · Interpretation

A critical guide to interpreting molecular docking scores. Why docking scores are not binding affinities, what they actually measure, how to validate with MD metrics, and what researchers should report in publications.

Read the complete article with tables, code and references on BioDockify.

Key References

• Trott, O. & Olson, A.J. AutoDock Vina. J. Comput. Chem. 31, 455-461 (2010).
• Li, H. et al. RF-Score v3. J. Cheminform. 12, 20 (2020).
• Jain, A.N. Scoring noncovalent protein-ligand interactions. Curr. Opin. Drug Discov. Devel. 7, 396-403 (2004).
• Hospital, A. et al. Molecular dynamics simulations: advances and applications. Adv. Appl. Bioinform. Chem. 8, 37-47 (2015).
• Sargsyan, K. et al. How to run and analyze molecular dynamics simulations. J. Chem. Inf. Model. 57, 284-290 (2017).

Scope & Limitations

Docking scores are NOT experimental binding affinities Correlation between scores and affinities is weak (R\u00B2 = 0.3\u20130.5) Consensus scoring reduces but does not eliminate errors