Breaking the polar-nonpolar division in solvation free energy prediction

Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies

(2017) Duc D. Nguyen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

ESES: Software for Eulerian solvent excluded surface

(2017) Beibei Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Feature functional theory–binding predictor (FFT–BP) for the blind prediction of binding free energies

(2017) Bao Wang et al.   THEORETICAL CHEMISTRY ACCOUNTS

Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies

(2016) Bao Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Parameter optimization in differential geometry based solvation models

(2015) Bao Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field

(2014) Silvia A. Martins et al.   Journal of Chemical Theory and Computation

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

(2014) Gerhard König et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Blind prediction of solvation free energies from the SAMPL4 challenge

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

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function

(2013) Lin Li et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Variational approach for nonpolar solvation analysis

(2012) Zhan Chen et al.   JOURNAL OF CHEMICAL PHYSICS

The SAMPL3 blind prediction challenge: transfer energy overview

(2012) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

DelPhi: a comprehensive suite for DelPhi software and associated resources

(2012) Lin Li et al.   BMC Biophysics

Differential geometry based solvation model. III. Quantum formulation

(2011) Zhan Chen et al.   JOURNAL OF CHEMICAL PHYSICS

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

Differential geometry based solvation model II: Lagrangian formulation

(2011) Zhan Chen et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Differential Geometry Based Multiscale Models

(2010) Guo-Wei Wei   BULLETIN OF MATHEMATICAL BIOLOGY

Differential geometry based solvation model I: Eulerian formulation

(2010) Zhan Chen et al.   JOURNAL OF COMPUTATIONAL PHYSICS

The SAMPL2 blind prediction challenge: introduction and overview

(2010) Matthew T. Geballe 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

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

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

Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

(2009) Aleksandr V. Marenich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Universal Approach to Solvation Modeling

(2008) Christopher J. Cramer et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

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