Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example

Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies

(2017) Giuseppe Deganutti et al.   Future Medicinal Chemistry

Crystal structure of the adenosine A2Areceptor bound to an antagonist reveals a potential allosteric pocket

(2017) Bingfa Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors

(2016) Dong Guo et al.   CHEMICAL REVIEWS

Deciphering the Complexity of Ligand–Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations

(2016) Alberto Cuzzolin et al.   Journal of Chemical Information and Modeling

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

5′-Substituted Amiloride Derivatives as Allosteric Modulators Binding in the Sodium Ion Pocket of the Adenosine A2A Receptor

(2016) Arnault Massink et al.   JOURNAL OF MEDICINAL CHEMISTRY

Binding Kinetics in Drug Discovery

(2016) Noelia Ferruz et al.   Molecular Informatics

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

(2016) Byron Carpenter et al.   NATURE

Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design

(2016) Arun Chandramohan et al.   PLoS Computational Biology

Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000

(2015) Giuseppe Deganutti et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors

(2015) Catherine F. Latham et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

From G Protein-coupled Receptor Structure Resolution to Rational Drug Design

(2015) Ali Jazayeri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks

(2015) Qiancheng Shen et al.   NUCLEIC ACIDS RESEARCH

Advances in Computational Techniques to Study GPCR–Ligand Recognition

(2015) Antonella Ciancetta et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Merging Allosteric and Active Site Binding Motifs: De novo Generation of Target Selectivity and Potency via Natural-Product-Derived Fragments

(2014) Jan Lanz et al.   ChemMedChem

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

(2014) Karl T. Debiec et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding

(2014) Henrik Keränen et al.   PLoS One

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

ASD v2.0: updated content and novel features focusing on allosteric regulation

(2013) Zhimin Huang et al.   NUCLEIC ACIDS RESEARCH

Fragment Screening of GPCRs Using Biophysical Methods: Identification of Ligands of the Adenosine A2A Receptor with Novel Biological Activity

(2012) Dan Chen et al.   ACS Chemical Biology

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

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine

(2011) Andrew S. Doré et al.   STRUCTURE

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

(2010) Maarten G. Wolf et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS