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Updated: May 26, 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
Transition network based on equilibrium sampling: a new method for extracting kinetic information from Monte Carlo
Konstantin V Klenin1, Wolfgang Wenzel
1Steinbuch Center for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany.
Abstract:
We propose a new type of transition network for modeling of protein dynamics. The nodes of the network correspond to the conformations taken from random sampling of equilibrium ensemble available, e.g., by Monte Carlo simulations. Although this approach does not provide absolute values of folding/unfolding rates, it allows identification of reaction pathways, transition state ensemble, and, eventually, intermediates. The new method is verified by a comparison with direct molecular dynamic simulations performed for a coarse-grained Gō-like model of proteins. As an illustrative example, we analyze kinetics of formation of a small β-hairpin (Trp zipper 1) in the all-atom representation.
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