Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

(2021) Evgeny Epifanovsky et al.   JOURNAL OF CHEMICAL PHYSICS

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

(2020) Andreas Krämer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Psi4 1.4: Open-source software for high-throughput quantum chemistry

(2020) Daniel G. A. Smith et al.   JOURNAL OF CHEMICAL PHYSICS

Membrane permeability of small molecules from unbiased molecular dynamics simulations

(2020) Andreas Krämer et al.   JOURNAL OF CHEMICAL PHYSICS

GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions

(2019) Christoph Bannwarth et al.   Journal of Chemical Theory and Computation

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

(2019) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method

(2018) Kyungreem Han et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods

(2018) Octav Caldararu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching

(2018) Phillip S. Hudson et al.   Journal of Chemical Theory and Computation

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale

(2018) Phillip S. Hudson et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

(2017) Minkyung Baek et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Overview of the SAMPL5 host–guest challenge: Are we doing better?

(2016) Jian Yin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

(2016) Juyong Lee et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Convergence of single-step free energy perturbation

(2016) Stefan Boresch et al.   MOLECULAR PHYSICS

Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching

(2015) Jicun Li 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

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

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

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

(2013) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases

(2012) Aleksandr V. Marenich et al.   Journal of Chemical Theory and Computation

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

(2012) Lee-Ping Wang et al.   Journal of Chemical Theory and Computation

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

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

Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method

(2012) Eric R. Pinnick et al.   THEORETICAL CHEMISTRY ACCOUNTS

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

(2011) Jan Řezáč et al.   Journal of Chemical Theory and Computation

Approaching post-Hartree–Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method

(2011) Feng Wang et al.   MOLECULAR SIMULATION

Communication: Hybrid ensembles for improved force matching

(2010) Lee-Ping Wang et al.   JOURNAL OF CHEMICAL PHYSICS

The quest for the best nonpolarizable water model from the adaptive force matching method

(2010) Omololu Akin-Ojo 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

Current Status of the AMOEBA Polarizable Force Field

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

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

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

(2008) Omololu Akin-Ojo 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

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

(2008) Jeng-Da Chai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS