ArticleJournal of chemical theory and computation2022
Granger Causality Analysis of Chignolin Folding.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 16 citations in OpenAlex.
- Directional information flow as a tool for analyzing protein allostery.bioRxiv : the preprint server for biology · 2026Article
- Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers.Journal of chemical theory and computation · 2026Article
- Probabilistic Forecasting for Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Data-driven enhanced sampling of mechanistic pathways.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Coupling causality and interpretable machine learning to reveal the reaction coordinate of C-N coupling with a supramolecular Cu-calix[8]arene catalyst.Digital discovery · 2025Article
- Developing a User-Friendly Code for the Fast Estimation of Well-Behaved Real-Space Partial Charges.Journal of chemical information and modeling · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Constantly advancing computer simulations of biomolecules provide huge amounts of data that are difficult to interpret. In particular, obtaining insights into functional aspects of macromolecular dynamics, often related to cascades of transient events, calls for methodologies that depart from the well-grounded framework of equilibrium statistical physics. One of the approaches toward the analysis of complex temporal data which has found applications in the fields of neuroscience and econometrics is Granger causality analysis. It allows determining which components of multidimensional time series are most influential for the evolution of the entire system, thus providing insights into causal relations within the dynamic structure of interest. In this work, we apply Granger analysis to a long molecular dynamics trajectory depicting repetitive folding and unfolding of a mini β-hairpin protein, CLN025. We find objective, quantitative evidence indicating that rearrangements within the hairpin turn region are determinant for protein folding and unfolding. On the contrary, interactions between hairpin arms score low on the causality scale. Taken together, these findings clearly favor the concept of zipperlike folding, which is one of two postulated β-hairpin folding mechanisms. More importantly, the results demonstrate the possibility of a conclusive application of Granger causality analysis to a biomolecular system.
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