Protein Preparation for Molecular Docking: A Research-Grade Workflow

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

How to prepare protein structures for molecular docking. Covers PDB cleanup, hydrogen addition, charge assignment, missing residues, disulfide bonds, and PDBQT conversion.

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

Key References

• Dolinsky, T.J. et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35, W522-W525 (2007).
• Jurrus, E. et al. Improvements to the APBS adaptive Poisson-Boltzmann solver. J. Chem. Theory Comput. 14, 1134-1148 (2018).

Scope & Limitations

Missing residues cannot be reliably modeled without homology modeling Alternate conformations require manual inspection Membrane proteins need special handling