ArticleJournal of chemical information and modeling2020
Validation of Free Energy Methods in AMBER.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Mining Druggable Sites in Influenza A Hemagglutinin: Binding of the Pinanamine-Based Inhibitor M090.ACS medicinal chemistry letters · 2025Article
- Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.Journal of chemical information and modeling · 2024Article
- Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.The journal of physical chemistry. B · 2024Article
- Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations.Journal of chemical information and modeling · 2024Article
- Calculated hydration free energies become less accurate with increases in molecular weight.PloS one · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA).Journal of chemical information and modeling · 2022Article
- Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.Journal of computational chemistry · 2022Article
- Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach.Journal of chemical theory and computation · 2022Article
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].Living journal of computational molecular science · 2022Article
- Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design.Pharmaceuticals (Basel, Switzerland) · 2021Review
- CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.Journal of chemical information and modeling · 2021Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.Journal of chemical theory and computation · 2020Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Herein we provide high-precision validation tests of the latest GPU-accelerated free energy code in AMBER. We demonstrate that consistent free energy results are obtained in both the gas phase and in solution. We first show, in the context of thermodynamic integration (TI), that the results are invariant with respect to "split" (e.g., stepwise decharge-vdW-recharge) versus "unified" protocols. This brought to light a subtle inconsistency in previous versions of AMBER that was traced to the improper treatment of 1-4 vdW and electrostatic interactions involving atoms across the softcore boundary. We illustrate that under the assumption that the ensembles produced by different legs of the alchemical transformation between molecules A and B in the gas phase and aqueous phase are very small, the inconsistency in the relative hydration free energy ΔΔ
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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.