SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

SAMPL7 blind predictions using nonequilibrium alchemical approaches

(2021) Piero Procacci et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Correcting electrostatic artifacts due to net‐charge changes in the calculation of ligand binding free energies

(2020) Christoph Öhlknecht et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

(2020) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2020) Conor D. Parks et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Assessing the accuracy of octanol–water partition coefficient predictions in the SAMPL6 Part II log P Challenge

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

Dielectric constant and density of aqueous alkali halide solutions by molecular dynamics: A force field assessment

(2020) Denis Saric et al.   JOURNAL OF CHEMICAL PHYSICS

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

(2020) Abhishek A. Kognole et al.   JOURNAL OF MOLECULAR MODELING

Spontaneous drying of non-polar deep-cavity cavitand pockets in aqueous solution

(2020) J. Wesley Barnett et al.   Nature Chemistry

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

(2020) Yuriy Khalak et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

(2019) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular recognition properties of acyclic cucurbiturils toward amino acids, peptides, and a protein

(2019) Sandra A. Zebaze Ndendjio et al.   SUPRAMOLECULAR CHEMISTRY

Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates

(2019) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

Binding Thermodynamics of Host–Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

(2019) David R. Slochower et al.   Journal of Chemical Theory and Computation

Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models

(2019) Alex Zhou et al.   Journal of Chemical Information and Modeling

Bind3P: Optimization of a Water Model Based on Host–Guest Binding Data

(2018) Jian Yin et al.   Journal of Chemical Theory and Computation

Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives

(2018) K. Kellett et al.   JOURNAL OF SOLUTION CHEMISTRY

Hybrid Molecular Container Based on Glycoluril and Triptycene: Synthesis, Binding Properties, and Triggered Release

(2018) Wenjin Liu et al.   CHEMISTRY-A EUROPEAN JOURNAL

A glycoluril dimer–triptycene hybrid receptor: synthesis and molecular recognition properties

(2018) Wenjin Liu et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Escaping Atom Types in Force Fields Using Direct Chemical Perception

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

Overview of the SAMPL6 host–guest binding affinity prediction challenge

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

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host–guest challenge via the AMOEBA polarizable force field

(2018) Marie L. Laury et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

pmx Webserver: A User Friendly Interface for Alchemistry

(2017) Vytautas Gapsys et al.   Journal of Chemical Information and Modeling

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host–Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters

(2017) Niel M. Henriksen et al.   Journal of Chemical Theory and Computation

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accuracy limit of rigid 3-point water models

(2016) Saeed Izadi et al.   JOURNAL OF CHEMICAL PHYSICS

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

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

(2016) Bradley Sherborne et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Concepts and protocols for electrostatic free energies

(2016) Thomas Simonson et al.   MOLECULAR SIMULATION

Binding Enthalpy Calculations for a Neutral Host–Guest Pair Yield Widely Divergent Salt Effects across Water Models

(2015) Kaifu Gao et al.   Journal of Chemical Theory and Computation

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate

(2015) Changsheng Zhang et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

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

Water: one molecule, two surfaces, one mistake

(2015) Carlos Vega   MOLECULAR PHYSICS

Some Practical Approaches to Treating Electrostatic Polarization of Proteins

(2014) Changge Ji et al.   ACCOUNTS OF CHEMICAL RESEARCH

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

(2014) Yen-Lin Lin et al.   Journal of Chemical Theory and Computation

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

(2014) David S. Cerutti et al.   Journal of Chemical Theory and Computation

Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

(2014) Jacob I. Monroe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

(2014) Thomas S. Peat et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL4 host–guest blind prediction challenge: an overview

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

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

(2013) Kai Wang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding of cyclic carboxylates to octa-acid deep-cavity cavitand

(2013) Corinne L. D. Gibb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

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

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors

(2012) A. Geoffrey Skillman   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

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

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

Release of High-Energy Water as an Essential Driving Force for the High-Affinity Binding of Cucurbit[n]urils

(2012) Frank Biedermann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

On understanding of the Hofmeister effect: how addition of salt alters the stability of temperature responsive polymers in aqueous solutions

(2012) Esben Thormann   RSC Advances

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions

(2011) Maria M. Reif et al.   JOURNAL OF CHEMICAL PHYSICS

Effect of the damping function in dispersion corrected density functional theory

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

Anion Binding to Hydrophobic Concavity Is Central to the Salting-in Effects of Hofmeister Chaotropes

(2011) Corinne L. D. Gibb et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Benzobis(imidazolium)-Cucurbit[8]uril Complexes for Binding and Sensing Aromatic Compounds in Aqueous Solution

(2010) Frank Biedermann et al.   CHEMISTRY-A EUROPEAN JOURNAL

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals—Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions

(2010) Lars Goerigk et al.   Journal of Chemical Theory and Computation

Acyclic Cucurbit[n]uril Congeners Are High Affinity Hosts

(2010) Da Ma et al.   JOURNAL OF ORGANIC CHEMISTRY

Analysis of Cooperativity by Isothermal Titration Calorimetry

(2009) Alan Brown   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

(2009) Peter Eastman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs 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

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

Guests of differing polarities provide insight into structural requirements for templates of water-soluble nano-capsules

(2009) Corinne L.D. Gibb et al.   TETRAHEDRON

Statistically optimal analysis of samples from multiple equilibrium states

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

Water Inside a Hydrophobic Cavitand Molecule

(2008) Jeffrey Ewell et al.   JOURNAL OF PHYSICAL CHEMISTRY B