ArticleScientific reports2022
Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- FLOWR.ROOT - A flow matching-based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction.Nature communications · 2026Article
- Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory.Journal of chemical information and modeling · 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
- Binding Free Energies without Alchemy.ArXiv · 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
- Generative Chemistry Platform for Small Molecules Targeting RNA: A Case Study for Chemical Optimization.Computational and structural biotechnology journal · 2026Article
- Article
- Hyperoside mitigates amphotericin B-induced nephrotoxicity in HK-2 cells via bioenergetic and oxidative stress modulation.BMC pharmacology & toxicology · 2025Article
- The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.Journal of chemical information and modeling · 2025Review
- 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
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Multilayered Computational Framework for Designing Peptide Inhibitors of HVEM-LIGHT Interaction.The journal of physical chemistry. B · 2024Article
- Computational Analysis of Heat Capacity Effects in Protein-Ligand Binding.Journal of chemical theory and computation · 2024Article
- Article
- Consensus holistic virtual screening for drug discovery: a novel machine learning model approach.Journal of cheminformatics · 2024Article
- On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations.Journal of chemical information and modeling · 2024Article
- Reporting the anti-neuroinflammatory potential of selected spondias mombin flavonoids through network pharmacology and molecular dynamics simulations.In silico pharmacology · 2024Article
- Drug repurposing against fucosyltransferase-2 via docking, STD-NMR, and molecular dynamic simulation studies.PloS one · 2024Article
- Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening.Communications chemistry · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We determined the effectiveness of absolute binding free energy (ABFE) calculations to refine the selection of active compounds in virtual compound screening, a setting where the more commonly used relative binding free energy approach is not readily applicable. To do this, we conducted baseline docking calculations of structurally diverse compounds in the DUD-E database for three targets, BACE1, CDK2 and thrombin, followed by ABFE calculations for compounds with high docking scores. The docking calculations alone achieved solid enrichment of active compounds over decoys. Encouragingly, the ABFE calculations then improved on this baseline. Analysis of the results emphasizes the importance of establishing high quality ligand poses as starting points for ABFE calculations, a nontrivial goal when processing a library of diverse compounds without informative co-crystal structures. Overall, our results suggest that ABFE calculations can play a valuable role in the drug discovery process.
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