Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

(2016) Ulf Ryde et al.   CHEMICAL REVIEWS

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials

(2016) Eric C. Dybeck et al.   Journal of Chemical Theory and Computation

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters

(2016) Pavlo O. Dral et al.   Journal of Chemical Theory and Computation

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

(2016) Xiangyu Jia et al.   Journal of Chemical Theory and Computation

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties

(2016) Pavlo O. Dral et al.   Journal of Chemical Theory and Computation

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level

(2016) Martin A. Olsson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

(2016) Frank C. Pickard et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations

(2015) Gerhard König et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes

(2015) Phillip S. Hudson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Efficient treatment of induced dipoles

(2015) Andrew C. Simmonett et al.   JOURNAL OF CHEMICAL PHYSICS

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

(2015) Gerhard König et al.   Journal of Chemical Theory and Computation

Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model

(2015) Samuel Genheden   Journal of Chemical Theory and Computation

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

(2015) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A “Stepping Stone” Approach for Obtaining Quantum Free Energies of Hydration

(2015) Chris Sampson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

(2015) Phillip S. Hudson et al.   Journal of Physical Chemistry Letters

Computational scheme for pH-dependent binding free energy calculation with explicit solvent

(2015) Juyong Lee et al.   PROTEIN SCIENCE

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald

(2014) Andrew C. Simmonett et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

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

Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation

(2014) Christopher Cave-Ayland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

(2013) Iakov Polyak et al.   JOURNAL OF CHEMICAL PHYSICS

Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes

(2013) Tobias Risthaus et al.   Journal of Chemical Theory and Computation

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

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

Thermodynamic integration to predict host-guest binding affinities

(2012) Morgan Lawrenz et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

(2012) Emilio Gallicchio 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

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Enhancing QM/MM Molecular Dynamics Sampling in Explicit Environments via an Orthogonal-Space-Random-Walk-Based Strategy

(2011) Donghong Min et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

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

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method

(2010) Stefan Bruckner 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

Elucidating Solvent Contributions to Solution Reactions with Ab Initio QM/MM Methods†

(2010) Hao Hu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Unorthodox uses of Bennett's acceptance ratio method

(2009) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations

(2009) Katherine E. Shaw et al.   Journal of Physical Chemistry Letters

LogD: Lipophilicity for ionisable compounds

(2008) Melanie Kah et al.   CHEMOSPHERE

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

(2008) Hao Hu et al.   JOURNAL OF CHEMICAL PHYSICS

Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach

(2008) Xiancheng Zeng et al.   JOURNAL OF CHEMICAL PHYSICS

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

(2008) Christopher J. Woods et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

(2008) Tell Tuttle et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Prediction of Partition Coefficients by Multiscale Hybrid Atomic-Level/Coarse-Grain Simulations

(2007) Julien Michel et al.   JOURNAL OF PHYSICAL CHEMISTRY B