Cross-Docking vs Redocking: What Each Protocol Proves (and What It Cannot)

By BioDockify Computational Research Team · October 17, 2026 · Molecular Docking

The two validation protocols of docking compared: redocking as protocol quality control, cross-docking as the honest simulation of real-world screening - setup, RMSD criteria, failure rates, and how to report both without overclaiming.

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
• Francoeur, P.G., Masuda, T., Sunseri, J. et al. Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design. J. Chem. Inf. Model. 60, 4200-4215 (2020). DOI: 10.1021/acs.jcim.0c00411
• Hou, X., Du, J., Liu, R. et al. Cross-docking benchmark for protein-ligand binding pose prediction. Sci. Data 11, 330 (2024).
• Verdonk, M.L., Cole, J.C., Hartshorn, M.J. et al. Improved protein-ligand docking using GOLD. Proteins 52, 609-623 (2003).

Scope & Limitations

Cross-docking success is target-dependent - pocket flexibility dominates; a protocol validated on one target does not transfer automatically RMSD under 2 A is a convention, not physics: 2 A at a small rigid pocket and 2 A at a flexible one certify different things