Dynamic Cross-Correlation Analysis of MD Trajectories

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

How to use Dynamic Cross-Correlation Maps (DCCM) to identify correlated and anti-correlated motions in protein MD simulations. Reveals allosteric communication pathways.

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

Key References

• Ichiye, T. & Karplus, M. Collective motions in proteins: a covariance analysis of atomic fluctuations. Proteins 11, 205-217 (1991).

Scope & Limitations

Linear correlation only — misses non-linear coupling Requires long simulations for stable correlation estimates Does not distinguish direct vs indirect coupling