ArticleJournal of chemical information and modeling2020
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS).
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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Unveiling the KRAS Relationship between Affinity and Dynamics: A Molecular Simulations Study.Journal of chemical information and modeling · 2026Article
- Article
- Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.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
- Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.Journal of chemical information and modeling · 2023Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules.Journal of chemical theory and computation · 2023Article
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
- ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom.Journal of chemical information and modeling · 2023Article
- Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules.Journal of chemical information and modeling · 2022Article
- Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.Journal of computer-aided molecular design · 2022Article
- Umbrella Sampling Simulations of Carbon Nanoparticles Crossing Immiscible Solvents.Molecules (Basel, Switzerland) · 2022Article
- Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder.Journal of chemical information and modeling · 2021Article
- Machine Learning for Electronically Excited States of Molecules.Chemical reviews · 2021Article
- On the Consistency of the Exfoliation Free Energy of Graphenes by Molecular Simulations.International journal of molecular sciences · 2021Article
- Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation.Chemical science · 2021Article
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.The journal of physical chemistry. A · 2021Article
- Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.The journal of physical chemistry. B · 2021Article
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Authors and funding
3 authors.
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Abstract
Free-energy perturbation (FEP) methods are commonly used in drug design to calculate relative binding free energies of different ligands to a common host protein. Alchemical ligand transformations are usually performed in multiple steps which need to be chosen carefully to ensure sufficient phase-space overlap between neighboring states. With one-step or single-step FEP techniques, a single reference state is designed that samples phase-space not only representative of a full transformation but also ideally resembles multiple ligand end states and hence allows for efficient multistate perturbations. Enveloping distribution sampling (EDS) is one example for such a method in which the reference state is created by a mathematical combination of the different ligand end states based on solid statistical mechanics. We have recently proposed a novel approach to EDS which enables efficient barrier crossing between the different end states, termed accelerated EDS (A-EDS). In this work, we further simplify the parametrization of the A-EDS reference state and demonstrate the automated calculation of multiple free-energy differences between different ligands from a single simulation in three different well-described drug design model systems.
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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.