ArticleJournal of chemical theory and computation2019
Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 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
- EWS-RNA Binding Protein 1: Structural Insights into Ewing Sarcoma by Conformational Dynamics Investigations.Current cancer drug targets · 2026Article
- Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0].Living journal of computational molecular science · 2025Article
- Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models.Proteomics · 2025Review
- Potentiation of the antimycobacterial activity of bedaquiline, clofazimine, and doxycycline againstOpen research Africa · 2025Article
- MPI-parallelization of the grid inhomogeneous solvation theory calculation.Journal of computational chemistry · 2024Article
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.Journal of chemical theory and computation · 2024Article
- PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.Journal of chemical information and modeling · 2023Article
- Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.The journal of physical chemistry letters · 2023Article
- Article
- Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data.Nature communications · 2023Article
- Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding.Journal of chemical theory and computation · 2023Article
- Total free energy analysis of fully hydrated proteins.Proteins · 2023Article
- 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
- Investigation on substrate specificity and catalytic activity of serine protease neuropsin.Biophysics and physicobiology · 2022Article
- Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves.Acta biomaterialia · 2021Article
- Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9).Scientific reports · 2021Article
- Review
- 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
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Authors and funding
5 authors.
Funding
Abstract
Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In substrate binding, but also in structure-based drug design, the thermodynamic properties of water molecules surrounding a given protein are of high interest. One of the main algorithms devised in recent years to quantify thermodynamic properties of water is the grid inhomogeneous solvation theory (GIST), which calculates these features on a grid surrounding the protein. Despite the inherent advantages of GIST, the computational demand is a major drawback, as calculations for larger systems can take days or even weeks. Here, we present a GPU accelerated version of the GIST algorithm, which facilitates efficient estimates of solvation free energy even of large biomolecular interfaces. Furthermore, we show that GIST can be used as a reliable tool to evaluate protein surface hydrophobicity. We apply the approach on a set of nine different proteases calculating localized solvation free energies on the surface of the binding interfaces as a measure of their hydrophobicity. We find a compelling agreement with the hydrophobicity of their substrates, i.e., peptides, binding into the binding cleft, and thus our approach provides a reliable description of hydrophobicity characteristics of these biological interfaces.
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