ArticleNature communications2020
Multisecond ligand dissociation dynamics from atomistic simulations.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- A theoretical framework for random acceleration molecular dynamics simulations.The Journal of chemical physics · 2026Article
- A Computational Modeling for Reconfigurable Biosensors.BioNanoScience · 2026Article
- More Sophisticated Is Not Always Better: A Comparison of Similarity Measures for Unsupervised Learning of Pathways in Biomolecular Simulations.The journal of physical chemistry. B · 2025Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- Advancing time-resolved structural biology: latest strategies in cryo-EM and X-ray crystallography.Nature methods · 2025Review
- How allosteric mutations control ligand binding in Lipocalin protein: odorant binding protein as a test case.Cellular and molecular life sciences : CMLS · 2025Article
- Dynamics and Stability Mechanism of Lactoferrin-EPA During Emulsification Process: Insights from Macroscopic and Molecular Perspectives.Foods (Basel, Switzerland) · 2025Article
- Data Generation for Machine Learning Interatomic Potentials and Beyond.Chemical reviews · 2024Review
- How specific ion effects influence the mechanical behaviors of amide macromolecules? A cross-scale study.RSC advances · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.Scientific reports · 2024Article
- Data-driven classification of ligand unbinding pathways.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- OneOPES, a Combined Enhanced Sampling Method to Rule Them All.Journal of chemical theory and computation · 2023Article
- Anisotropic Friction in a Ligand-Protein Complex.Nano letters · 2023Article
- Recalibrating the calcium trap in amino acid carboxyl groupsPhysical chemistry chemical physics : PCCP · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and rate-limiting steps in protein-ligand unbinding is crucial for modern drug discovery. To achieve the enhanced sampling, we perform dissipation-corrected targeted molecular dynamics simulations, which yield free energy and friction profiles of molecular processes under consideration. Subsequently, we use these fields to perform temperature-boosted Langevin simulations which account for the desired kinetics occurring on multisecond timescales and beyond. Adopting the dissociation of solvated sodium chloride, trypsin-benzamidine and Hsp90-inhibitor protein-ligand complexes as test problems, we reproduce rates from molecular dynamics simulation and experiments within a factor of 2-20, and dissociation constants within a factor of 1-4. Analysis of friction profiles reveals that binding and unbinding dynamics are mediated by changes of the surrounding hydration shells in all investigated systems.
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