Overview of the SAMPL6 host–guest binding affinity prediction challenge

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

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

The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation

(2018) Nupur Bansal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SAMPL6 host–guest challenge: binding free energies via a multistep approach

(2018) Yiğitcan Eken et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge

(2018) Michail Papadourakis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach

(2018) Piero Procacci et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

(2018) Lin Frank Song 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

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges

(2018) Naohiro Nishikawa et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Cucurbit[8]uril•guest complexes: blinded dataset for the SAMPL6 challenge

(2018) Steven Murkli et al.   SUPRAMOLECULAR CHEMISTRY

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

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

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

(2017) Bernd Kuhn et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2017) Peter Eastman et al.   PLoS Computational Biology

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

(2017) Mohammad M. Sultan et al.   Scientific Reports

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

(2016) Stefano Bosisio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Absolute binding free energies for octa-acids and guests in SAMPL5

(2016) Florentina Tofoleanu 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

Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands

(2016) Matthew R. Sullivan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics

(2016) Soumendranath Bhakat 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

On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

(2016) Nupur Bansal et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

(2016) Rajat Kumar Pal et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)

(2016) Octav Caldararu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Synthesis of Water-Soluble Deep-Cavity Cavitands

(2016) Matthew B. Hillyer et al.   ORGANIC LETTERS

Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field

(2016) David R. Bell et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework

(2016) Piero Procacci   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands

(2016) Francesca Nerattini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

KECSA-Movable Type Implicit Solvation Model (KMTISM)

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

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

(2015) Niel M. Henriksen 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

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

(2015) Jian Yin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Binding Hydrated Anions with Hydrophobic Pockets

(2015) Punidha Sokkalingam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

(2015) Juyong Lee et al.   PROTEIN SCIENCE

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

(2014) Andrew D. White 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

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

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

Blind prediction of HIV integrase binding from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics

(2014) Ya-Wen Hsiao 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

The SAMPL4 host–guest blind prediction challenge: an overview

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

Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme

(2014) Manuel Neeb et al.   JOURNAL OF MEDICINAL CHEMISTRY

Acyclic Cucurbit[n]uril-type Molecular Containers: Influence of Aromatic Walls on their Function as Solubilizing Excipients for Insoluble Drugs

(2014) Ben Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions

(2013) Zheng Zheng et al.   Journal of Chemical Information and Modeling

The Movable Type Method Applied to Protein–Ligand Binding

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

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

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

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

Absolute and relative binding affinity of cucurbit[7]uril towards a series of cationic guests

(2013) Liping Cao et al.   SUPRAMOLECULAR CHEMISTRY

Who cares for the protons?

(2012) Paul Czodrowski   BIOORGANIC & MEDICINAL CHEMISTRY

On the Role of Dewetting Transitions in Host–Guest Binding Free Energy Calculations

(2012) Kathleen E. Rogers 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 binding affinities: evaluating the accuracy of generalized force-fields

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

FRED and HYBRID docking performance on standardized datasets

(2012) Mark McGann   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

FRED Pose Prediction and Virtual Screening Accuracy

(2011) Mark McGann   Journal of Chemical Information and Modeling

Nonmonotonic Assembly of a Deep-Cavity Cavitand

(2011) Haiying Gan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New Ultrahigh Affinity Host−Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations

(2011) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

(2011) Jianing Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

(2010) Boris Aguilar et al.   BIOPHYSICAL JOURNAL

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

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

Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields

(2010) Martin Korth   Journal of Chemical Theory and Computation

SAMPL2 challenge: prediction of solvation energies and tautomer ratios

(2010) A. Geoffrey Skillman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL2 blind prediction challenge: introduction and overview

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

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

(2010) Jeremy R. Greenwood et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Acyclic Cucurbit[n]uril Congeners Are High Affinity Hosts

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

Current Status of the AMOEBA Polarizable Force Field

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

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

(2009) Jan Řezáč et al.   Journal of Chemical Theory and Computation

The AGBNP2 Implicit Solvation Model

(2009) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

(2009) J. Peter Guthrie   JOURNAL OF PHYSICAL CHEMISTRY B

Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and Design

(2009) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts 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

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

(2008) Alan P. Graves et al.   JOURNAL OF MOLECULAR BIOLOGY

Water Inside a Hydrophobic Cavitand Molecule

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