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

Glycoluril-Derived Molecular Clips are Potent and Selective Receptors for Cationic Dyes in Water

(2016) Nengfang She et al.   CHEMISTRY-A EUROPEAN JOURNAL

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

The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

(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

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

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

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular containers assembled through the hydrophobic effect

(2015) Jacobs H. Jordan et al.   CHEMICAL SOCIETY REVIEWS

The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes

(2015) Jérémie Mortier et al.   DRUG DISCOVERY TODAY

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

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data

(2015) Lauren Wickstrom et al.   JOURNAL OF MOLECULAR RECOGNITION

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

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

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

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

(2014) Andrew T. Fenley et al.   Journal of Chemical Theory and Computation

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

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

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Molecular Recognition and Ligand Association

(2013) Riccardo Baron et al.   Annual Review of Physical Chemistry

Guest-mediated switching of the assembly state of a water-soluble deep-cavity cavitand

(2013) Haiying Gan et al.   CHEMICAL COMMUNICATIONS

Virtual Screening Strategies in Drug Discovery: A Critical Review

(2013) A. Lavecchia et al.   CURRENT MEDICINAL CHEMISTRY

Natural triple excitations in local coupled cluster calculations with pair natural orbitals

(2013) Christoph Riplinger et al.   JOURNAL OF CHEMICAL PHYSICS

The Movable Type Method Applied to Protein–Ligand Binding

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

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction

(2013) Camilo Velez-Vega et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory

(2012) Stefan Grimme   CHEMISTRY-A EUROPEAN JOURNAL

From Laptop to Benchtop to Bedside: Structure-based Drug Design on Protein Targets

(2012) Lu Chen et al.   CURRENT DRUG METABOLISM

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

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

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

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

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Gazing into the crystal ball; the future of computer-aided drug design

(2011) Eric Martin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Lysine-Specific Molecular Tweezers Are Broad-Spectrum Inhibitors of Assembly and Toxicity of Amyloid Proteins

(2011) Sharmistha Sinha et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities

(2010) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

The SAMPL2 blind prediction challenge: introduction and overview

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

The AGBNP2 Implicit Solvation Model

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

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