ArticleJournal of computer-aided molecular design2017
The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Diels-Alder Reactions in [PdInorganic chemistry · 2026Article
- Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint.Biophysical journal · 2024Article
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies.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
- Catalysis by [GaChemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- An overview of the SAMPL8 host-guest binding challenge.Journal of computer-aided molecular design · 2022Article
- On the Nature of Guest Complexation in Water: Triggered Wetting-Water-Mediated Binding.The journal of physical chemistry. B · 2022Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [MJournal of chemical information and modeling · 2021Article
- Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.The Journal of chemical physics · 2021Article
- The role of water in host-guest interaction.Nature communications · 2021Article
- Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites.Journal of chemical theory and computation · 2020Article
- Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters.Journal of chemical theory and computation · 2020Article
- Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development.Journal of chemical theory and computation · 2019Article
- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.Journal of computer-aided molecular design · 2019Review
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.Journal of chemical theory and computation · 2018Article
- HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.The journal of physical chemistry. B · 2017Article
- Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment.The journal of physical chemistry. B · 2017Article
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4 authors.
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Abstract
The absolute binding free energies and binding enthalpies of twelve host-guest systems in the SAMPL5 blind challenge were computed using our attach-pull-release (APR) approach. This method has previously shown good correlations between experimental and calculated binding data in retrospective studies of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) systems. In the present work, the computed binding free energies for host octa acid (OA or OAH) and tetra-endo-methyl octa-acid (TEMOA or OAMe) with guests are in good agreement with prospective experimental data, with a coefficient of determination (R
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