ArticleJournal of chemical theory and computation2020
Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Buffer Region Embedding for Hybrid Machine-Learned/Molecular-Mechanical Simulations in Complex Environments.Journal of chemical information and modeling · 2026Article
- Probing Limitations of Co-Alchemical Charge Changes in Free-Energy Calculations.Journal of chemical theory and computation · 2025Article
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations.Journal of chemical information and modeling · 2025Article
- Impact of confining hydrogen molecule inside fullerenes: A glance through DFT study.Journal of molecular modeling · 2024Article
- BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost 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
- Guidelines for Free-Energy Calculations Involving Charge Changes.Journal of chemical theory and computation · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough.Journal of chemical information and modeling · 2023Article
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
- Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder.Journal of chemical information and modeling · 2021Article
- Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation.Scientific reports · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
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Authors and funding
4 authors.
Funding
Abstract
Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein-protein complexes. Alchemical methods, on the other hand, are preferably applied for small ligands that bind to deeply buried binding sites. The latter methods are also widely known to be heavily artifacted by the representation of electrostatic energies in periodic simulation boxes, in particular, when net-charge changes are involved. Different methods have been described to deal with these artifacts, including postsimulation correction schemes and instantaneous correction schemes (e.g., co-alchemical perturbation of ions). Here, we use very simple test systems to show that instantaneous correction schemes with no change in the system net charge lower the artifacts but do not eliminate them. Furthermore, we show that free energies from pathway methods suffer from the same artifacts.
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