Binding-Site Identification and Grid Box Selection for Molecular Docking

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

How to identify binding sites and select grid boxes for molecular docking. Covers pocket detection tools, grid box sizing, centering strategies, and blind docking vs site-specific docking.

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

Key References

• Le Guilloux, V. et al. Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics 10, 168 (2009).
• Trott, O. & Olson, A.J. AutoDock Vina. J. Comput. Chem. 31, 455-461 (2010).

Scope & Limitations

Automatic pocket detection may miss allosteric sites Grid box too small may clip the ligand Grid box too large wastes computation