ArticleThe Journal of chemical physics2016
How wet should be the reaction coordinate for ligand unbinding?
Article in The Journal of chemical physics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- The Maximum Caliber Variational Principle for Nonequilibria.Annual review of physical chemistry · 2020Review
- A new approach to estimate atomic energies.Journal of molecular modeling · 2019Article
- Past-future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics.Nature communications · 2019Article
- Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.Journal of chemical information and modeling · 2018Article
- Predicting reaction coordinates in energy landscapes with diffusion anisotropy.The Journal of chemical physics · 2017Article
- How and when does an anticancer drug leave its binding site?Science advances · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.
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Registered trials
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