Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

Testing automatic methods to predict free binding energy of host–guest complexes in SAMPL7 challenge

(2021) Dylan Serillon et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2021) Martin Amezcua et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL7 blind predictions using nonequilibrium alchemical approaches

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

People systematically overlook subtractive changes

(2021) Gabrielle S. Adams et al.   NATURE

Evaluation of consensus scoring methods for AutoDock Vina, smina and idock

(2020) Lily Masters et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Crowdsourcing drug discovery for pandemics

(2020) John Chodera et al.   Nature Chemistry

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

(2020) A. Acharya et al.   Journal of Chemical Information and Modeling

Facile synthesis of a diverse library of mono-3-substituted β-cyclodextrin analogues

(2019) K. Kellett et al.   SUPRAMOLECULAR CHEMISTRY

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

(2018) Changsheng Zhang et al.   Journal of Chemical Theory and Computation

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

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi 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

Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

(2017) Piero Procacci et al.   Journal of Chemical Theory and Computation

Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to

(2017) Piero Procacci   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

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

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

(2015) Niel M. Henriksen et al.   Journal of Chemical Theory and Computation

Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations

(2015) Robert B. Sandberg et al.   Journal of Chemical Theory and Computation

SAMPL4 & DOCK3.7: lessons for automated docking procedures

(2014) Ryan G. Coleman 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

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

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

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

(2012) Matthew P. Repasky 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

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Gaining confidence in high-throughput screening

(2012) J. Bibette   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alchemical free energy methods for drug discovery: progress and challenges

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

Open Babel: An open chemical toolbox

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

Good Practices in Free-Energy Calculations

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris 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