ArticleJournal of chemical theory and computation2016
Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.
Article in Journal of chemical theory and computation, 2016. 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.
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0].Living journal of computational molecular science · 2025Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Spatially Resolved Hydration Thermodynamics in Biomolecular Systems.The journal of physical chemistry. B · 2022Review
- 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
- An ATPase with a twist: A unique mechanism underlies the activity of the bacterial tyrosine kinase, Wzc.Science advances · 2021Article
- Spatially resolved free-energy contributions of native fold and molten-globule-like Crambin.Biophysical journal · 2021Article
- 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
- Per|Mut: Spatially Resolved Hydration Entropies from Atomistic Simulations.Journal of chemical theory and computation · 2021Article
- Article
- Utilizing Grand Canonical Monte Carlo Methods in Drug Discovery.ACS medicinal chemistry letters · 2020Article
- A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site.PloS one · 2019Article
- 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
- High-Temperature Dynamic Behavior in Bulk Liquid Water: A Molecular Dynamics Simulation Study using the OPC and TIP4P-Ew Potentials.Frontiers of physics · 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
- Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations.The journal of physical chemistry. B · 2017Article
- 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
- Enthalpic and Entropic Contributions to Hydrophobicity.Journal of chemical theory and computation · 2016Article
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3 authors.
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Abstract
A number of computational tools available today compute the thermodynamic properties of water at surfaces and in binding pockets by using inhomogeneous solvation theory (IST) to analyze explicit-solvent simulations. Such methods enable qualitative spatial mappings of both energy and entropy around a solute of interest and can also be applied quantitatively. However, the entropy estimates of existing methods have, to date, been almost entirely limited to the first-order terms in the IST's entropy expansion. These first-order terms account for localization and orientation of water molecules in the field of the solute but not for the modification of water-water correlations by the solute. Here, we present an extension of the Grid Inhomogeneous Solvation Theory (GIST) approach which accounts for water-water translational correlations. The method involves rewriting the two-point density of water in terms of a conditional density and utilizes the efficient nearest-neighbor entropy estimation approach. Spatial maps of this second order term, for water in and around the synthetic host cucurbit[7]uril and in the binding pocket of the enzyme Factor Xa, reveal mainly negative contributions, indicating solute-induced water-water correlations relative to bulk water; particularly strong signals are obtained for sites at the entrances of cavities or pockets. This second-order term thus enters with the same, negative, sign as the first order translational and orientational terms. Numerical and convergence properties of the methodology are examined.
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