Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

Protein–Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals

(2020) Tobias Hüfner-Wulsdorf et al.   Journal of Chemical Information and Modeling

Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method

(2019) Yoshiki Ishii et al.   Journal of Chemical Theory and Computation

Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces

(2019) Johannes Kraml et al.   Journal of Chemical Theory and Computation

Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

(2017) Guilherme Duarte Ramos Matos et al.   JOURNAL OF CHEMICAL AND ENGINEERING DATA

Testing inhomogeneous solvation theory in structure-based ligand discovery

(2017) Trent E. Balius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

(2016) Steven Ramsey et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

(2016) Shota Uehara et al.   MOLECULES

Spatial Decomposition of Translational Water–Water Correlation Entropy in Binding Pockets

(2015) Crystal N. Nguyen et al.   Journal of Chemical Theory and Computation

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations

(2015) Camilo Velez-Vega et al.   Journal of Chemical Theory and Computation

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein–Ligand Binding: Binding Site Variability

(2015) E. Prabhu Raman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm

(2014) David J. Huggins   Journal of Chemical Theory and Computation

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa

(2014) Crystal N. Nguyen et al.   Journal of Chemical Theory and Computation

Rapid estimation of hydration thermodynamics of macromolecular regions

(2013) E. Prabhu Raman et al.   JOURNAL OF CHEMICAL PHYSICS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Assessing the Accuracy of Inhomogeneous Fluid Solvation Theory in Predicting Hydration Free Energies of Simple Solutes

(2013) David J. Huggins et al.   JOURNAL OF PHYSICAL CHEMISTRY B

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

(2012) Crystal N. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods

(2008) Vladimir Hnizdo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY