ArticleThe journal of physical chemistry. B2013
Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Deep GIST: Deep Learning Models for Predicting the Distribution of Hydration Thermodynamics around Proteins.Journal of chemical information and modeling · 2026Article
- Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures.Journal of computer-aided molecular design · 2022Article
- Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.Journal of chemical theory and computation · 2021Article
- Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.Journal of chemical theory and computation · 2020Article
- Applications of water molecules for analysis of macromolecule properties.Computational and structural biotechnology journal · 2020Review
- The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.Journal of chemical theory and computation · 2018Article
- Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.Journal of chemical theory and computation · 2018Article
- On the accuracy of one- and two-particle solvation entropies.The Journal of chemical physics · 2017Article
- Relationship between Solvation Thermodynamics from IST and DFT Perspectives.The journal of physical chemistry. B · 2017Review
- Studying the role of cooperative hydration in stabilizing folded protein states.Journal of structural biology · 2016Article
- Enthalpic and Entropic Contributions to Hydrophobicity.Journal of chemical theory and computation · 2016Article
- Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.The journal of physical chemistry. B · 2016Article
- Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.Journal of chemical theory and computation · 2016Article
- Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions.Chemistry & biology · 2015Review
- Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.Journal of chemical theory and computation · 2015Article
- Quantifying the entropy of binding for water molecules in protein cavities by computing correlations.Biophysical journal · 2015Article
- Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects.Journal of cheminformatics · 2015Article
- Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation.Journal of computational chemistry · 2014Article
- Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.Journal of chemical information and modeling · 2013Article
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2 authors.
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Abstract
Accurate prediction of hydration free energies is a key objective of any free energy method that is applied to modeling and understanding interactions in the aqueous phase. Inhomogeneous fluid solvation theory (IFST) is a statistical mechanical method for calculating solvation free energies by quantifying the effect of a solute acting as a perturbation to bulk water. IFST has found wide application in understanding hydration phenomena in biological systems, but quantitative applications have not been comprehensively assessed. In this study, we report the hydration free energies of six simple solutes calculated using IFST and independently using free energy perturbation (FEP). This facilitates a validation of IFST that is independent of the accuracy of the force field. The results demonstrate that IFST shows good agreement with FEP, with an R(2) coefficient of determination of 0.99 and a mean unsigned difference of 0.7 kcal/mol. However, sampling is a major issue that plagues IFST calculations and the results suggest that a histogram method may require prohibitively long simulations to achieve convergence of the entropies, for bin sizes which effectively capture the underlying probability distributions. Results also highlight the sensitivity of IFST to the reference interaction energy of a water molecule in bulk, with a difference of 0.01 kcal/mol changing the predicted hydration free energies by approximately 2.4 kcal/mol for the systems studied here. One of the major advantages of IFST over perturbation methods such as FEP is that the systems are spatially decomposed to consider the contribution of specific regions to the total solvation free energies. Visualizing these contributions can yield detailed insights into solvation thermodynamics. An insight from this work is the identification and explanation of regions with unfavorable free energy density relative to bulk water. These regions contribute unfavorably to the hydration free energy. Further work is necessary before IFST can be extended to yield accurate predictions of binding free energies, but the work presented here demonstrates its potential.
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