ArticleJournal of chemical theory and computation2018
Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.
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 17 papers.
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Who cites it
17 citing papers in PubMed, 58 citations in OpenAlex.
- Free energy simulations on a biomimetic glucose receptor: understanding the selectivity of GluHUT.Chemical science · 2026Article
- Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.Mini reviews in medicinal chemistry · 2024Review
- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.The journal of physical chemistry. A · 2022Article
- Binding of synthetic carbohydrate receptors to enveloped virus glycans: Insights from molecular dynamics simulations.Carbohydrate research · 2022Article
- SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.Journal of chemical information and modeling · 2022Article
- Micellar Composition Affects Lipid Accretion Kinetics in Molecular Dynamics Simulations: Support for Lipid Network Reproduction.Life (Basel, Switzerland) · 2022Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.Frontiers in molecular biosciences · 2022Review
- Diffusivity ofFluid phase equilibria · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics.Journal of chemical theory and computation · 2020Article
- Inclusion Complexation of Organic Micropollutants with β-Cyclodextrin.The journal of physical chemistry. B · 2020Article
- Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.The journal of physical chemistry. B · 2019Article
- Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?Journal of chemical theory and computation · 2019Article
- Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.The journal of physical chemistry letters · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-time-scale molecular dynamics (MD) simulations, postanalysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of k
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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.