ArticleLiving journal of computational molecular science2020
Best Practices for Alchemical Free Energy Calculations [Article v1.0].
Article in Living journal of computational molecular science, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers.
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Who cites it
172 citing papers in PubMed.
- Parameterization of the CHARMM force field for divalent cations (Ca2+/Be2+) binding to anionic lipids with isothermal titration calorimetry.The Journal of chemical physics · 2026Article
- Alchemical Free Energy Perturbation Predicts Relative Binding Affinities of Propofol Analogs and Etomidate Stereoisomers at the GABAACS omega · 2026Article
- Physical priors improve performance of structure-based binding affinity models.bioRxiv : the preprint server for biology · 2026Article
- Toward Relative Redox Potential Predictions in Flavoproteins: Treatment of a Charge-Changing Mutation in Alchemical Free Energy Simulations.Journal of chemical theory and computation · 2026Article
- Dual-Coordinate Relative Free Energy Simulations Using Machine-Learned Interatomic Potentials.Journal of chemical theory and computation · 2026Article
- Computational Characterization of Ligand Recognition and Inhibition in a 1,4-Dioxane-Degrading Propane Monooxygenase.Journal of chemical information and modeling · 2026Article
- Kinase inhibitors can change protonation or tautomeric state upon binding.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking Docking Protocols on Predicting Alternative Binding Modes.Journal of chemical information and modeling · 2026Article
- FLOWR.ROOT - A flow matching-based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction.Nature communications · 2026Article
- MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change.Journal of chemical information and modeling · 2026Article
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- Scalable Boltzmann generators for equilibrium sampling of large-scale materials.Nature communications · 2026Article
- Dynamic mechanism for subtype selectivity of endocannabinoids.The Journal of biological chemistry · 2026Article
- The Last Mile Problem: A Critical Assessment of Physics-Based and AI Tools for Small Molecule Binding Prediction in Virtual Screening.Journal of chemical information and modeling · 2026Article
- NEMAT: An Automated Nonequilibrium Free-Energy Framework for Predicting Ligand Affinity in Membrane Proteins.Journal of chemical information and modeling · 2026Article
- How to Use Quantum Computers for Biomolecular Free Energies.Journal of chemical theory and computation · 2026Article
- Machine-Learned Electrostatic Potentials for Accurate Hydration Free Energy Calculations.Journal of chemical theory and computation · 2026Article
- Comparative Assessment of Free Energy Computational Methods for Revealing the Interactions Driving PARP1 Selective Inhibition.Journal of chemical information and modeling · 2026Article
- Uncertainty Quantification forChemical reviews · 2026Review
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
112 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy functions representing
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.