ArticleJournal of chemical theory and computation2018
Uncertainty Quantification in Alchemical Free Energy Methods.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
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- Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR.Journal of chemical theory and computation · 2026Article
- Uncertainty Quantification forChemical reviews · 2026Review
- Effects of doping and functionalization on black phosphorus nanosheets for enhanced quercetin delivery.RSC advances · 2025Article
- Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations.Journal of chemical information and modeling · 2025Article
- Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2025Article
- Robust Automated Truncation Point Selection for Molecular Simulations.Journal of chemical theory and computation · 2025Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations.Journal of chemical theory and computation · 2024Article
- Accelerating COVID-19 Drug Discovery with High-Performance Computing.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions.Journal of chemical theory and computation · 2023Article
- Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.Journal of chemical information and modeling · 2023Article
- Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.Journal of chemical theory and computation · 2023Article
- TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal.Journal of chemical information and modeling · 2023Article
- Article
- Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?Molecules (Basel, Switzerland) · 2022Article
- Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules.PNAS nexus · 2022Article
- Alchemical Free Energy Calculations to Investigate Protein-Protein Interactions: the Case of the CDC42/PAK1 Complex.Journal of chemical information and modeling · 2022Article
- The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.Scientific reports · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.
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