ArticlePloS one2019
A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
- Decoding BCL6 Inhibitors: Computational Insights into the Impact of Water Networks on Potency.Journal of chemical information and modeling · 2025Article
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set.Journal of chemical information and modeling · 2025Article
- Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism.Molecules (Basel, Switzerland) · 2024Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Total free energy analysis of fully hydrated proteins.Proteins · 2023Article
- Spatially Resolved Hydration Thermodynamics in Biomolecular Systems.The journal of physical chemistry. B · 2022Review
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- 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
- Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features.Computational and mathematical methods in medicine · 2022Article
- Contributions of higher-order proximal distribution functions to solvent structure around proteins.The Journal of chemical physics · 2021Article
- Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.International journal of molecular sciences · 2021Review
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.Journal of computer-aided molecular design · 2020Article
- Distribution and Function of Glycosaminoglycans and Proteoglycans in the Development, Homeostasis and Pathology of the Ocular Surface.Frontiers in cell and developmental biology · 2020Review
- Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces.Journal of chemical theory and computation · 2019Article
- Hydration of Aromatic Heterocycles as an Adversary of π-Stacking.Journal of chemical information and modeling · 2019Article
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site.
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