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- W4289366615 abstract "A key overall goal of biomolecular simulations is the characterization of mechanism -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the ensemble of pathways, in direct analogy to thermal configurational ensembles. Quantification of that heterogeneity is essential to a complete understanding of mechanism. We propose a general approach for characterizing path ensembles based on mapping individual trajectories into pathway classes whose populations and uncertainties can be analyzed as an ordinary histogram, providing a quantitative fingerprint of mechanism. In contrast to prior flux-based analyses used for discrete-state models, stochastic deviations from average behavior are explicitly included via direct classification of trajectories. The histogram approach, furthermore, is applicable to analysis of continuous trajectories. It enables straightforward comparison between ensembles produced by different methods or under different conditions. To implement the formulation, we develop approaches for classifying trajectories, including a clustering-based approach suitable for both continuous-space (e.g., molecular dynamics) or discrete-state (e.g., Markov state model) trajectories, as well as a fundamental sequence approach tailored for discrete-state trajectories but also applicable to continuous trajectories through a mapping process. We apply the pathway histogram analysis to a toy model and an extremely long atomistic molecular dynamics trajectory of protein folding." @default.
- W4289366615 created "2022-08-02" @default.
- W4289366615 creator A5003813944 @default.
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- W4289366615 date "2018-10-24" @default.
- W4289366615 modified "2023-09-23" @default.
- W4289366615 title "Pathway Histogram Analysis of Trajectories: A general strategy for quantification of molecular mechanisms" @default.
- W4289366615 doi "https://doi.org/10.48550/arxiv.1810.10514" @default.
- W4289366615 hasPublicationYear "2018" @default.
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