ArticleJournal of chemical theory and computation2018
Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.
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 18 papers.
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Who cites it
18 citing papers in PubMed.
- Inclusion Complexation of Native and Functionalized α-, β-, and γ-Cyclodextrins with PFAS: An Experimental and Molecular Simulation Study.The journal of physical chemistry. B · 2026Article
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Using Deep Graph Neural Networks Improves Physics-Based Hydration Free Energy Predictions Even for Molecules Outside of the Training Set Distribution.The journal of physical chemistry. B · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins.Physical chemistry chemical physics : PCCP · 2024Article
- Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment.Journal of chemical theory and computation · 2024Article
- Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024Article
- 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
- Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization.Journal of chemical theory and computation · 2023Article
- 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
- Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds.Physical chemistry chemical physics : PCCP · 2021Article
- Diffusivity ofFluid phase equilibria · 2021Article
- SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.Journal of computer-aided molecular design · 2021Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Inclusion Complexation of Organic Micropollutants with β-Cyclodextrin.The journal of physical chemistry. B · 2020Article
- Overview of the SAMPL6 host-guest binding affinity prediction challenge.Journal of computer-aided molecular design · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host-guest systems, along with pure liquid properties. Tests of Bind3P against >100 experimental binding free energies and enthalpies for host-guest systems distinct from the training set show a consistent drop in the mean signed error, relative to matched calculations with TIP3P. Importantly, Bind3P also yields some improvement in the hydration free energies of small organic molecules and preserves the accuracy of bulk water properties, such as density and the heat of vaporization. The same approach can be applied to more sophisticated water models that can better represent pure water properties. These results lend further support to the concept of integrating host-guest binding data into force field parametrization.
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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.