ArticleJournal of chemical theory and computation2024
Automated Adaptive Absolute Binding Free Energy Calculations.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- 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
- Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR.Journal of chemical theory and computation · 2026Article
- EasyDock 1.3: An Automated Pipeline for Molecular Docking.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
- Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection.Journal of chemical theory and computation · 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
- Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders.International journal of molecular sciences · 2026Review
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand Reorganization.The journal of physical chemistry. B · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Quantum mechanics in drug design: Progress, challenges, and future frontiers.Communicative & integrative biology · 2026Review
- Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo.Nature communications · 2025Article
- Article
- Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations.Journal of chemical information and modeling · 2025Article
- Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease.Digital discovery · 2025Article
- Discovery of Novel Pyridin-2-yl Urea Inhibitors Targeting ASK1 Kinase and Its Binding Mode by Absolute Protein-Ligand Binding Free Energy Calculations.International journal of molecular sciences · 2025Article
- Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data.Communications chemistry · 2025Article
- Robust Automated Truncation Point Selection for Molecular Simulations.Journal of chemical theory and computation · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in drug discovery, but are often prohibitively computationally expensive. To unlock their potential, efficient automated ABFE workflows are required to reduce both computational cost and human intervention. We present a fully automated ABFE workflow based on the automated selection of λ windows, the ensemble-based detection of equilibration, and the adaptive allocation of sampling time based on inter-replicate statistics. We find that the automated selection of intermediate states with consistent overlap is rapid, robust, and simple to implement. Robust detection of equilibration is achieved with a paired
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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.