ArticleFrontiers in molecular biosciences2022
Local Ion Densities can Influence Transition Paths of Molecular Binding.
Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 5 citations in OpenAlex.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm.Journal of computational chemistry · 2023Article
- Water regulates the residence time of Benzamidine in Trypsin.Nature communications · 2022Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Improper reaction coordinates can pose significant problems for path-based binding free energy calculations. Particularly, omission of long timescale motions can lead to over-estimation of the energetic barriers between the bound and unbound states. Many methods exist to construct the optimal reaction coordinate using a pre-defined basis set of features. Although simulations are typically conducted in explicit solvent, the solvent atoms are often excluded by these feature sets-resulting in little being known about their role in reaction coordinates, and ultimately, their role in determining (un)binding rates and free energies. In this work, analysis is done on an extensive set of host-guest unbinding trajectories, working to characterize differences between high and low probability unbinding trajectories with a focus on solvent-based features, including host-ion interactions, guest-ion interactions and location-dependent ion densities. We find that differences in ion densities as well as guest-ion interactions strongly correlate with differences in the probabilities of reactive paths that are used to determine free energies of (un)binding and play a significant role in the unbinding process.
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