Batch Docking: 100 Ligands Against One Protein — Complete Workflow

By BioDockify Computational Research Team · August 10, 2026 · Batch Docking

A complete workflow for batch docking 100 ligands against a single protein target. Covers input preparation, per-ligand grid boxes, failure handling, consensus ranking, and reproducibility.

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

Key References

• Trott, O. & Olson, A.J. AutoDock Vina. J. Comput. Chem. 31, 455-461 (2010).
• Wilkinson, M.D. et al. The FAIR Guiding Principles. Sci. Data 3, 160018 (2016).

Scope & Limitations

Each ligand runs sequentially — 100 ligands take ~15-30 minutes Ligand quality affects results — bad inputs produce bad outputs Grid box is shared across all ligands (same binding site)