Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables
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Updated: May 13, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
J Juraszek1, G Saladino, T S van Erp
1Spanish National Cancer Research Centre, CNIO, calle Melchor Fernandez Almagro 3, 28029 Madrid, Spain.
Abstract:
Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interface sampling with the optimal interfaces and free-energy profiles provided by path collective variables makes the rate calculation for practical biological applications feasible and efficient. This methodology can reproduce the experimental rate constant of Trp-cage miniprotein folding with the same level of accuracy as transition path sampling at a fraction of the cost.
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