ArticleJournal of chemical theory and computation2015
Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 134 citations in OpenAlex.
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- LamNet: an alchemical-path-aware graph neural network to accelerate binding free energy calculations for drug discovery and beyond.National science review · 2026Article
- Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands.Journal of chemical theory and computation · 2025Article
- Partially Sulfated Pillar[5]Arenes: Synthesis and Molecular Recognition Properties.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition.Communications biology · 2024Article
- Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA.Nature communications · 2024Article
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies.Chemical science · 2023Article
- Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems.Journal of chemical information and modeling · 2023Article
- The role of loop dynamics in the prediction of ligand-protein binding enthalpy.Chemical science · 2023Article
- AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.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
- An overview of the SAMPL8 host-guest binding challenge.Journal of computer-aided molecular design · 2022Article
- Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.Scientific reports · 2022Article
- Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.Journal of chemical theory and computation · 2021Article
- Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [MJournal of chemical information and modeling · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van't Hoff equation. Excellent agreement between the direct and van't Hoff methods is demonstrated for both host-guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design.
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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.