ArticleJournal of chemical information and modeling2022
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Reliability of AI Methods in Drug Discovery: Evaluation of Boltz-2 for Structure and Binding Affinity Prediction.Journal of chemical theory and computation · 2026Article
- Selecting medical research data platforms for translational biomedical research: a five-tier overview and requirement-weighted assessment framework.Frontiers in digital health · 2026Review
- Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2025Article
- Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction.Nature communications · 2024Article
- Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations.Journal of chemical theory and computation · 2024Article
- Ensemble-Based Approaches Ensure Reliability and Reproducibility.Journal of chemical information and modeling · 2023Article
- Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions.Journal of chemical theory and computation · 2023Article
- The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.Scientific reports · 2022Article
- Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility.Journal of chemical theory and computation · 2022Article
- Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols.Journal of chemical theory and computation · 2022Article
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Authors and funding
7 authors.
Funding
Abstract
Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.
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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.