ArticleJournal of chemical theory and computation2025
ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- One Blob to Rule Them All: A Universal Dual-Topology Nonequilibrium Framework for Relative and Absolute Binding Free Energies via a Lennard-Jones Blob Reference.Journal of chemical theory and computation · 2026Article
- Dual-Coordinate Relative Free Energy Simulations Using Machine-Learned Interatomic Potentials.Journal of chemical theory and computation · 2026Article
- Toward Predicting Solubility of Arbitrary Solutes in Arbitrary Solvents: Prediction of Density and Refractive Index Using Machine Learning Algorithms with Global Sensitivity Analysis.Organic process research & development · 2026Article
- Predicting Solvation Free Energies of Molecules and Ions via First-Principles and Machine-Learning Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Integrative Network Pharmacology and Molecular Docking Analysis Reveals the Multitarget Mechanisms of Pterostilbene in Neurodegenerative Diseases.Pharmaceuticals (Basel, Switzerland) · 2026Article
- PrimaDORAC: An improved Web Interface for Rapid GAFF2 Parameter Assignment with ABCG2 Charge Models for Drug Design Applications.Journal of computational chemistry · 2026Article
- Antidiabetic Potential ofMolecules (Basel, Switzerland) · 2026Article
- Development and Test of Highly Accurate End Point Free Energy Methods. 4. Expanding Solvents Capability and logBB Prediction.The journal of physical chemistry. B · 2026Article
- Assessment and Optimization of Force Fields for Glycine Polymorphism and Solution Properties.Journal of chemical theory and computation · 2026Article
- Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.Acta crystallographica. Section D, Structural biology · 2026Article
- Computing Solvation Free Energies of Small Molecules with Experimental Accuracy.Journal of the American Chemical Society · 2026Article
- A novel nanotherapeutic strategy: rescuing nucleus pulposus cells from fatty acid metabolic disorder and pyroptosis through ACOT13 by Chinese herbal formula nanoparticles.Journal of nanobiotechnology · 2026Article
- A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.Journal of chemical information and modeling · 2026Article
- Architecture-Independent Absolute Solvation Free Energy Calculations with Neural Network Potentials.The journal of physical chemistry letters · 2025Article
- Evaluation of the ABCG2 Charge Model in Protein-Ligand Binding Free-Energy Calculations.Journal of chemical information and modeling · 2025Article
- Leveraging Molecular Mechanics With the uESE Continuum Solvation Model for Efficient Solvation Free Energy Prediction: Impact of Conformation and Extensive Validation.Journal of computational chemistry · 2025Article
- Transferable Neural Network Potentials and Condensed Phase Properties.Journal of chemical information and modeling · 2025Article
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
- Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.bioRxiv : the preprint server for biology · 2025Article
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5 authors.
Funding
Abstract
In this report, we describe the development and validation of ABCG2, a new charge model with milestone free energy accuracy, while allowing instantaneous atomic charge assignment for arbitrary organic molecules. In combination with the second-generation general AMBER force field (GAFF2), ABCG2 led to a root-mean-square error (RMSE) of 0.99 kcal/mol on the hydration free energy calculation of all 642 solutes in the FreeSolv database, for the first time meeting the chemical accuracy threshold through physics-based molecular simulation against the golden-standard data set. Against the Minnesota Solvation Database, the solvation free energy calculation on 2068 pairs of a range of organic solutes in diverse solvents led to an RMSE of 0.89 kcal/mol. The 1913 data points of transfer free energies from the aqueous solution to organic solvents obtained an RMSE of 0.85 kcal/mol, corresponding to 0.63 log units for logP. The benchmark on densities of neat liquids for 1839 organic molecules and heat of vaporizations of 874 organic liquids achieved a comparable performance with the default restrained electrostatic potential (RESP) charge method of GAFF2. The fluctuations of assigned partial atomic charges over different input conformations from ABCG2 are demonstrated to be much smaller than those of RESP from statistics of 96 real drug molecules. The validation results demonstrated not only the accuracy but also the transferability and generality of the GAFF2/ABCG2 combination.
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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.