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

Octanol–water partition coefficient measurements for the SAMPL6 blind prediction challenge

(2020) Mehtap Işık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Dynamics Simulations of Membrane Permeability

(2019) Richard M. Venable et al.   CHEMICAL REVIEWS

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

(2019) Andreas Krämer et al.   Journal of Chemical Theory and Computation

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

(2019) Zhi Yue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches

(2019) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

(2018) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Escaping Atom Types in Force Fields Using Direct Chemical Perception

(2018) David L. Mobley et al.   Journal of Chemical Theory and Computation

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

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge

(2018) Samarjeet Prasad et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Mapping the Drude polarizable force field onto a multipole and induced dipole model

(2017) Jing Huang et al.   JOURNAL OF CHEMICAL PHYSICS

Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry

(2017) Billy J. Williams-Noonan et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2017) Peter Eastman et al.   PLoS Computational Biology

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

(2016) Ignacio Soteras Gutiérrez et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Computer Modeling of Halogen Bonds and Other σ-Hole Interactions

(2016) Michal H. Kolář et al.   CHEMICAL REVIEWS

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

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

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

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predictions of the physicochemical properties of amino acid side chain analogs using molecular simulation

(2016) Alauddin Ahmed et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Robustness in the fitting of molecular mechanics parameters

(2015) Kenno Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Automated parameterization of intermolecular pair potentials using global optimization techniques

(2014) Andreas Krämer et al.   COMPUTER PHYSICS COMMUNICATIONS

The SAMPL4 host–guest blind prediction challenge: an overview

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

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

Rapid parameterization of small molecules using the force field toolkit

(2013) Christopher G. Mayne et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Solubility of Water in Octan-1-ol from (275 to 369) K

(2012) Brian E. Lang   JOURNAL OF CHEMICAL AND ENGINEERING DATA

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

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

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

Imaging Molecular Transport across Lipid Bilayers

(2011) Su Li et al.   BIOPHYSICAL JOURNAL

MATCH: An atom-typing toolset for molecular mechanics force fields

(2011) Joseph D. Yesselman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Let’s get honest about sampling

(2011) David L. Mobley   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

The SAMPL2 blind prediction challenge: introduction and overview

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

Good Practices in Free-Energy Calculations

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

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

Let’s not forget tautomers

(2009) Yvonne Connolly Martin   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

Statistically optimal analysis of samples from multiple equilibrium states

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