Clustering Protein-Ligand MD Trajectories

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

How to cluster MD trajectory frames by structural similarity. Covers RMSD-based clustering, k-medoids, and identifying dominant conformational states for drug design.

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

Key References

• Daura, X. et al. Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. 38, 236-240 (1999).
• Shao, J. et al. Clustering of molecular dynamics trajectories. J. Chem. Theory Comput. 3, 2312-2334 (2007).

Scope & Limitations

Clustering quality depends on cutoff choice Different algorithms give different results Does not capture transition pathways