ArticleJournal of chemical information and modeling2022
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.
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 31 papers.
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Who cites it
31 citing papers in PubMed.
- Discovery of a novel STING-binding peptide associated with reduced cGAMP-induced inflammatory gene expression.Journal of enzyme inhibition and medicinal chemistry · 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
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model.Journal of chemical theory and computation · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Ligand-Binding Free Energy Simulations of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- In silico-driven protocol for hit-to-lead optimization: a case study on PDE9A inhibitors.Journal of computer-aided molecular design · 2025Article
- Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction.Bioinformatics (Oxford, England) · 2025Article
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.Journal of chemical information and modeling · 2025Article
- Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations.The journal of physical chemistry. B · 2024Article
- Machine-learned molecular mechanics force fields from large-scale quantum chemical data.Chemical science · 2024Article
- Embracing exascale computing in nucleic acid simulations.Current opinion in structural biology · 2024Review
- The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.The journal of physical chemistry. B · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.Journal of chemical information and modeling · 2024Article
- Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations.Journal of chemical theory and computation · 2024Article
- What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.Journal of chemical theory and computation · 2024Article
- Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling.Nature communications · 2023Article
- Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.Journal of chemical information and modeling · 2023Article
- Alchemical Free Energy Calculations on Membrane-Associated Proteins.Journal of chemical theory and computation · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nowadays, drug design projects benefit from highly accurate protein-ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.
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