Docking Methods Section Template: Write It So Anyone Can Reproduce You

By BioDockify Computational Research Team · October 11, 2026 · Academic Writing

A copy-paste molecular docking methods section with every element a reviewer expects: target provenance, preparation, ligand handling, grid definition, protocol parameters, analysis and statistics - with a worked filled-in example.

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

Key References

• Trott, O. & Olson, A.J. AutoDock Vina. J. Comput. Chem. 31, 445-461 (2010). DOI: 10.1002/jcc.21334
• Morris, G.M., Huey, R., Lindstrom, W. et al. AutoDock4 and AutoDockTools4. J. Comput. Chem. 30, 2785-2791 (2009). DOI: 10.1002/jcc.21256
• Eberhardt, J., Santos-Martins, D., Tillack, A.F. & Forli, S. AutoDock Vina 1.2.0. J. Chem. Inf. Model. 61, 3891-3898 (2021). DOI: 10.1021/acs.jcim.1c00203
• Daina, A., Michielin, O. & Zoete, V. SwissADME. J. Med. Chem. 60, 598-620 (2017). DOI: 10.1021/acs.jmedchem.6b01804

Scope & Limitations

Journals differ in structural preferences; adapt section order to your target journal's recent computational papers The template covers standard rigid/flexible docking; covalent docking, water-inclusive protocols, and ensemble docking need additional parameters reported