ArticleScientific reports2019
Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Antimicrobial peptides as computational candidates for SARS-CoV-2 papain-like protease inhibition.Scientific reports · 2026Article
- Reliability of AI Methods in Drug Discovery: Evaluation of Boltz-2 for Structure and Binding Affinity Prediction.Journal of chemical theory and computation · 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
- Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction.Bioinformatics (Oxford, England) · 2025Article
- Synthetic Retinoids for the Modulation of Genomic and Nongenomic Processes in Neurodegenerative Diseases.ACS omega · 2025Article
- Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2025Article
- Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.Nature communications · 2023Article
- PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications.Scientific data · 2022Article
- The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.Scientific reports · 2022Article
- Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors.Journal of chemical information and modeling · 2022Article
- ReliableJournal of chemical information and modeling · 2022Article
- Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease.Molecular systems design & engineering · 2022Article
- Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers.Interface focus · 2021Article
- Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- The effect of protein mutations on drug binding suggests ensuing personalised drug selection.Scientific reports · 2021Article
- Uncertainty quantification in classical molecular dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors.Interface focus · 2020Article
- Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.Interface focus · 2020Review
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
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Authors and funding
6 authors.
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Abstract
As the application of computational methods in drug discovery pipelines becomes more widespread it is increasingly important to understand how reproducible their results are and how sensitive they are to choices made in simulation setup and analysis. Here we use ensemble simulation protocols, termed ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent), to investigate the sensitivity of the popular molecular mechanics Poisson-Boltzmann surface area (MMPBSA) methodology. Using the bromodomain-containing protein 4 (BRD4) system bound to a diverse set of ligands as our target, we show that robust rankings can be produced only through combining ensemble sampling with multiple trajectories and enhanced solvation via an explicit ligand hydration shell.
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