Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities

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

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

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

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

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

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

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems

(2014) Maximilian Kubillus et al.   Journal of Chemical Theory and Computation

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

(2014) Michael Gaus 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

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

(2014) Alexander J. Sodt et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications

(2014) Xiya Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

(2014) Yihan Shao et al.   MOLECULAR PHYSICS

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

(2013) Christoph Dellago et al.   Entropy

Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

(2013) Lei Huang et al.   Journal of Chemical Theory and Computation

New faster CHARMM molecular dynamics engine

(2013) Antti-Pekka Hynninen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies

(2013) Anita de Ruiter et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Frontiers in free-energy calculations of biological systems

(2013) Christophe Chipot   Wiley Interdisciplinary Reviews-Computational Molecular Science

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields

(2012) James F. Matthews et al.   Journal of Chemical Theory and Computation

Parametrization and Benchmark of DFTB3 for Organic Molecules

(2012) Michael Gaus et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

(2012) Steve Kaminski et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

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

Free energy calculations of protein–ligand interactions

(2011) Anita de Ruiter et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

MSCALE: A General Utility for Multiscale Modeling

(2011) H. Lee Woodcock et al.   Journal of Chemical Theory and Computation

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

Use of a QM/MM-Based FEP Method to Evaluate the Anomalous Hydration Behavior of Simple Alkyl Amines and Amides: Application to the Design of FBPase Inhibitors for the Treatment of Type-2 Diabetes

(2011) M. Rami Reddy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration

(2010) Stefan Bruckner 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

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM: The biomolecular simulation program

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

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

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

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

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution

(2008) Marat Valiev et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA