How to Identify a Stable Protein-Ligand Complex from MD Simulation

By BioDockify Computational Research Team · August 9, 2026 · MD Analysis

A practical guide to evaluating protein-ligand binding stability from MD simulation results. Covers RMSD, H-bond persistence, binding free energy, and validation criteria.

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

Key References

• Bruce Macdonell et al. Molecular dynamics simulations for rational drug design. Curr. Opin. Struct. Biol. 75, 102386 (2022).
• Genheden, S. & Ryde, U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin. Drug Discov. 10, 449-461 (2015).
• Homeyer, N. & Gohlke, H. Free energy calculations by the MM/PBSA method. Mol. Inform. 31, 114-122 (2012).

Scope & Limitations

Stability criteria depend on the specific system 10ns may not capture slow unbinding events Stable binding != high affinity