ArticleJournal of chemical theory and computation2024
Alchemical Enhanced Sampling with Optimized Phase Space Overlap.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization.Journal of chemical information and modeling · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- LamNet: an alchemical-path-aware graph neural network to accelerate binding free energy calculations for drug discovery and beyond.National science review · 2026Article
- SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations.The journal of physical chemistry. B · 2025Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.Journal of chemical information and modeling · 2025Article
- Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations.Journal of chemical information and modeling · 2025Article
- Adaptive Lambda Scheduling: A Method for Computational Efficiency in Free Energy Perturbation Simulations.Journal of chemical information and modeling · 2025Article
- Multiple Topology Replica Exchange of Expanded Ensembles for Multidimensional Alchemical Calculations.Journal of chemical theory and computation · 2025Article
- Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.Journal of chemical information and modeling · 2024Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate importance sampling in free energy simulations. The method achieves enhanced sampling from Hamiltonian replica exchange within a dual topology framework while utilizing new smoothstep softcore potentials. A common sampling problem encountered in lead optimization is the functionalization of aromatic rings that exhibit distinct conformational preferences when interacting with the protein. It is difficult to converge the distribution of ring conformations due to the long time scale of ring flipping events; however, the ACES method addresses this issue by modeling the
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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.