ArticleThe Journal of chemical physics2013
Rapid estimation of hydration thermodynamics of macromolecular regions.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
- 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
- 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
- Article
- Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.Journal of chemical theory and computation · 2016Article
- Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability.Journal of the American Chemical Society · 2015Article
- Quantifying the entropy of binding for water molecules in protein cavities by computing correlations.Biophysical journal · 2015Article
- Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa.Journal of chemical theory and computation · 2014Article
- Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations.Journal of chemical theory and computation · 2014Article
- Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation.Journal of computational chemistry · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
This work describes a novel protocol to efficiently calculate the local free energy of hydration of specific regions in macromolecules. The method employs Monte Carlo simulations in the grand canonical ensemble to generate water configurations in a selected spherical region in the macromolecule. Excess energy and entropy of hydration are calculated by analyzing the water configurational distributions following the recently published grid inhomogeneous solvation theory method [C. N. Nguyen, T. K. Young, and M. K. Gilson, J. Chem. Phys. 137, 044101 (2012)]. Our method involves the approximations of treating the macromolecule and distant solvent as rigid and performing calculations on multiple such conformations to account for conformational diversity. These approximations are tested against water configurations obtained from a molecular dynamics simulation. The method is validated by predicting the number and location of water molecules in 5 pockets in the protein Interleukin-1β for which experimental water occupancy data are available. Free energy values are validated against decoupling free energy perturbation calculations. The results indicate that the approximations used in the method enable efficient prediction of free energies of water displacement.
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