How to Select a Protein Structure for Molecular Docking
By BioDockify Computational Research Team · August 8, 2026 · Selection
A practical guide to selecting the right protein structure for molecular docking. Covers resolution, apo vs holo structures, crystal vs cryo-EM vs AlphaFold, and multi-chain considerations.
Read the complete article with tables, code and references on BioDockify.
Key References
- Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
- Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583-589 (2021).
- Varadi, M. et al. AlphaFold Protein Structure Database. Nucleic Acids Res. 50, D439-D444 (2022).
Scope & Limitations
Crystal structures represent a single conformation — not the full dynamics AlphaFold structures are predictions, not experimental measurements Multi-chain complexes may require special handling