FreeSolv: a database of experimental and calculated hydration free energies, with input files

Blind prediction of solvation free energies from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration

(2014) Christopher J. Fennell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

(2013) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

High-Throughput Prediction of the Hydration Free Energies of Small Molecules from a Classical Density Functional Theory

(2013) Yu Liu et al.   Journal of Physical Chemistry Letters

Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

(2012) Boris Aguilar et al.   Journal of Chemical Theory and Computation

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

(2012) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering

(2012) Lianqing Zheng et al.   Journal of Chemical Theory and Computation

Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models

(2012) Abhishek Mukhopadhyay et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biomolecular electrostatics and solvation: a computational perspective

(2012) Pengyu Ren et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

(2011) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test

(2011) Charles W. Kehoe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Alchemical prediction of hydration free energies for SAMPL

(2011) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Modeling aqueous solvation with semi-explicit assembly

(2011) C. J. Fennell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

(2010) Traian Sulea et al.   Journal of Chemical Theory and Computation

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

(2010) Christopher R. Corbeil et al.   Journal of Chemical Theory and Computation

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

(2010) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Validating CHARMM Parameters and Exploring Charge Distribution Rules in Structure-Based Drug Design

(2009) Jennifer L. Knight et al.   Journal of Chemical Theory and Computation

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

(2009) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

The AGBNP2 Implicit Solvation Model

(2009) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

The SAMP1 Solvation Challenge: Further Lessons Regarding the Pitfalls of Parametrization†

(2009) Anthony Nicholls et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

(2009) J. Peter Guthrie   JOURNAL OF PHYSICAL CHEMISTRY B

Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions

(2009) Christopher J. Fennell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations†

(2009) David L. Mobley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Just Size

(2009) Christopher J. Fennell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

(2008) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY

Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules

(2008) David L. Mobley et al.   JOURNAL OF PHYSICAL CHEMISTRY B