ArticleJournal of chemical theory and computation2018
Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 51 citations in OpenAlex.
- Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR.Journal of chemical theory and computation · 2026Article
- A Quadrupolar Fullerene Model System for Benchmarking Enhanced Sampling of Trapped Waters in Free Energy Calculations.The journal of physical chemistry. B · 2026Article
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Decoding BCL6 Inhibitors: Computational Insights into the Impact of Water Networks on Potency.Journal of chemical information and modeling · 2025Article
- Advancing Binding Affinity Calculations: A Non-Equilibrium Simulations Approach for Calculation of Relative Binding Free Energies in Systems with Trapped Waters.Journal of chemical theory and computation · 2025Article
- Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.Journal of chemical information and modeling · 2025Article
- Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo.Nature communications · 2025Article
- Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters.Journal of chemical theory and computation · 2024Article
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- The maximal and current accuracy of rigorous protein-ligand binding free energy calculations.Communications chemistry · 2023Article
- GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.Journal of computational chemistry · 2023Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- Synthesis, molecular docking, and binding Gibbs free energy calculation of β-nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease.Journal of molecular structure · 2023Article
- Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules.Journal of chemical theory and computation · 2023Article
- Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.Journal of chemical theory and computation · 2023Article
- Water Networks in Complexes between Proteins and FDA-Approved Drugs.Journal of chemical information and modeling · 2023Article
- Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data.Journal of chemical information and modeling · 2022Article
- Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.Journal of computer-aided molecular design · 2022Article
- Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks.ACS physical chemistry Au · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Computational methods to calculate ligand binding affinities are increasing in popularity, due to improvements in simulation algorithms, computational resources, and easy-to-use software. However, issues can arise in relative ligand binding free energy simulations if the ligands considered have different active site water networks, as simulations are typically performed with a predetermined number of water molecules (fixed N ensembles) in preassigned locations. If an alchemical perturbation is attempted where the change should result in a different active site water network, the water molecules may not be able to adapt appropriately within the time scales of the simulations-particularly if the active site is occluded. By combining the grand canonical ensemble (μVT) to sample active site water molecules, with conventional alchemical free energy methods, the water network is able to dynamically adapt to the changing ligand. We refer to this approach as grand canonical alchemical perturbation (GCAP). In this work we demonstrate GCAP for two systems; Scytalone Dehydratase (SD) and Adenosine A
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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.