Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

(2020) Shunzhou Wan et al.   Interface Focus

An online resource for GPCR structure determination and analysis

(2019) Christian Munk et al.   NATURE METHODS

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders

(2019) Andrew Potterton et al.   Journal of Chemical Theory and Computation

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

(2019) David W. Wright et al.   Scientific Reports

Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor

(2018) Noureldin Saleh et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Uncertainty Quantification in Alchemical Free Energy Methods

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs?

(2018) Krishna Sriram et al.   MOLECULAR PHARMACOLOGY

Chemical Diversity in the G Protein-Coupled Receptor Superfamily

(2018) Márton Vass et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Structure of the adenosine-bound human adenosine A1 receptor–Gi complex

(2018) Christopher J. Draper-Joyce et al.   NATURE

Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

(2017) Shunzhou Wan et al.   Journal of Chemical Information and Modeling

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands

(2017) Noureldin Saleh et al.   Journal of Chemical Information and Modeling

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study

(2017) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

An Ensemble-Based Protocol for the Computational Prediction of Helix–Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics

(2017) Nojood A. Altwaijry et al.   Journal of Chemical Theory and Computation

Equilibrium and kinetic selectivity profiling on the human adenosine receptors

(2016) Dong Guo et al.   BIOCHEMICAL PHARMACOLOGY

Relative Binding Free Energy Calculations Applied to Protein Homology Models

(2016) Daniel Cappel et al.   Journal of Chemical Information and Modeling

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

(2016) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

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

Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength

(2016) Elena Segala et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure of the adenosine A2A receptor bound to an engineered G protein

(2016) Byron Carpenter et al.   NATURE

On the calculation of equilibrium thermodynamic properties from molecular dynamics

(2016) Peter V. Coveney et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structure-kinetics relationships of Capadenoson derivatives as adenosine A 1 receptor agonists

(2015) Julien Louvel et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

FESetup: Automating Setup for Alchemical Free Energy Simulations

(2015) Hannes H. Loeffler et al.   Journal of Chemical Information and Modeling

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

(2015) Hui Sun Lee et al.   Journal of Chemical Theory and Computation

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

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

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Scintillation proximity assay (SPA) as a new approach to determine a ligand’s kinetic profile. A case in point for the adenosine A1 receptor

(2015) Lizi Xia et al.   Purinergic Signalling

Molecular mechanism of allosteric modulation at GPCRs: insight from a binding kinetics study at the human A1adenosine receptor

(2014) Dong Guo et al.   BRITISH JOURNAL OF PHARMACOLOGY

Binding Kinetics of ZM241385 Derivatives at the Human Adenosine A2AReceptor

(2014) Dong Guo et al.   ChemMedChem

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors

(2014) Lars Boukharta et al.   PLoS Computational Biology

Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time

(2012) Dong Guo et al.   BRITISH JOURNAL OF PHARMACOLOGY

Ensemble of G Protein-Coupled Receptor Active States

(2012) P. S.-H. Park   CURRENT MEDICINAL CHEMISTRY

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

(2011) S. Wan et al.   Journal of the Royal Society Interface

Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases

(2010) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

The properties of thermostabilised G protein-coupled receptors (StaRs) and their use in drug discovery

(2010) Nathan Robertson et al.   NEUROPHARMACOLOGY

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Langevin thermostat for rigid body dynamics

(2009) Ruslan L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases

(2008) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY