ReviewACS medicinal chemistry letters2023
Recent Advances in Alchemical Binding Free Energy Calculations for Drug Discovery.
Review in ACS medicinal chemistry letters, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
- Rational design of triazole tyrosinase inhibitors via integrated free energy calculations.Molecular diversity · 2026Article
- Free energy perturbation and machine learning-assisted identification of potential MAP3K8 hit molecules: a comprehensive structure- and ligand-based studies.Molecular diversity · 2026Article
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.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
- Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.Communications chemistry · 2026Article
- Identification of Potential Pancreatic Lipase Inhibitors from Traditional Chinese Medicines via Molecular Docking, Molecular Dynamics Simulation and In Vitro Validation.Current issues in molecular biology · 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
- Spectrochemical, medicinal, and toxicological studies of moxifloxacin and its novel analogs: a quantum chemistry and drug discovery approach.RSC advances · 2026Article
- Generative Chemistry Platform for Small Molecules Targeting RNA: A Case Study for Chemical Optimization.Computational and structural biotechnology journal · 2026Article
- MnM-W-MMGBSA: A Computational Strategy to Improve Relative Binding Free Energies of Protein-Protein Interaction Systems.The journal of physical chemistry. B · 2025Article
- How many crystal structures do you need to trust your docking results?bioRxiv : the preprint server for biology · 2025Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- A free energy perturbation-assisted machine learning strategy for mimotope screening in neoantigen-based vaccine design.Briefings in bioinformatics · 2025Article
- The Quasi-Bound State as a Predictor of Relative Binding Free Energy.Journal of chemical information and modeling · 2025Article
- Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations.Journal of chemical information and modeling · 2025Article
- Oral ENPP1 inhibitor designed using generative AI as next generation STING modulator for solid tumors.Nature communications · 2025Article
- A Thermodynamic Cycle to Predict the Competitive Inhibition Outcomes of an Evolving Enzyme.Journal of chemical theory and computation · 2025Article
- Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands.Journal of chemical theory and computation · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rigorous physics-based methods to calculate binding free energies of protein-ligand complexes have become a valued component of structure-based drug design. Relative and absolute binding free energy calculations have been deployed prospectively in support of solving diverse drug discovery challenges. Here we review recent applications of binding free energy calculations to fragment growing and linking, scaffold hopping, binding pose validation, virtual screening, covalent enzyme inhibition, and positional analogue scanning. Furthermore, we discuss the merits of using protein models and highlight recent efforts to replace costly binding free energy calculations with predictions from machine learning models trained on a limited number of free energy perturbation or thermodynamic integration calculations thereby allowing for extended chemical space exploration.
Identifiers
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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.