Ligand Preparation for Molecular Docking: Protonation, Tautomers, Charges and Conformers
By BioDockify Computational Research Team · August 8, 2026 · Preparation
A research-grade guide to ligand preparation for molecular docking. Covers protonation states, tautomer enumeration, partial charge assignment, and 3D conformer generation using RDKit and OpenBabel.
Read the complete article with tables, code and references on BioDockify.
Key References
- Landrum, G. RDKit: Open-source cheminformatics. https://www.rdkit.org
- O'Boyle, N.M. et al. Open Babel: An open chemical toolbox. J. Cheminform. 3, 33 (2011).
- Jakalian, A. et al. Fast, efficient generation of high-quality atomic charges. J. Comput. Chem. 21, 105-120 (2000).
Scope & Limitations
Protonation state prediction is approximate — experimental pKa values are more reliable Tautomer enumeration may miss rare tautomers AM1-BCC charges are semi-empirical approximations