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

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

(2014) Gerhard König et al.   Journal of Chemical Theory and Computation

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered

(2014) J. Peter Guthrie   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

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

(2014) Paulius Mikulskis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Absolute Hydration Free Energies of Blocked Amino Acids: Implications for Protein Solvation and Stability

(2013) Gerhard König et al.   BIOPHYSICAL JOURNAL

Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies

(2013) Stephen J. Fox et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Partial atomic charges and their impact on the free energy of solvation

(2012) Joakim P. M. Jämbeck et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set

(2012) Jens Reinisch et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL3 blind prediction challenge: transfer energy overview

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

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

(2012) Jimmy Heimdal et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations

(2011) Gerhard König et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field

(2011) Oliver Beckstein 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

A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations

(2011) Frank R. Beierlein et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Practically Efficient QM/MM Alchemical Free Energy Simulations: The Orthogonal Space Random Walk Strategy

(2010) Donghong Min et al.   Journal of Chemical Theory and Computation

Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules

(2010) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The SAMPL2 blind prediction challenge: introduction and overview

(2010) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction test of free energies of hydration with COSMO-RS

(2010) Andreas Klamt et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models

(2010) Raphael F. Ribeiro 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

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

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough

(2009) Gerhard König et al.   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

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

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

Density Functionals with Broad Applicability in Chemistry

(2008) Yan Zhao 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