Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models

A Unified Model of the GABAA Receptor Comprising Agonist and Benzodiazepine Binding Sites

(2013) Rikke Bergmann et al.   PLoS One

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

GABA Binding to an Insect GABA Receptor: A Molecular Dynamics and Mutagenesis Study

(2012) Jamie A. Ashby et al.   BIOPHYSICAL JOURNAL

Ligand-Gated Ion Channels: New Insights into Neurological Disorders and Ligand Recognition

(2012) Damien Lemoine et al.   CHEMICAL REVIEWS

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Molecular actions of smoking cessation drugs at  4 2 nicotinic receptors defined in crystal structures of a homologous binding protein

(2012) B. Billen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sampling protein motion and solvent effect during ligand binding

(2012) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pentameric ligand-gated ion channel ELIC is activated by GABA and modulated by benzodiazepines

(2012) R. Spurny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Pharmacology of Pentameric Receptor Channels: From Bacteria to Brain

(2012) Pierre-Jean Corringer et al.   STRUCTURE

Two Amino Acid Residues Contribute to a Cation-  Binding Interaction in the Binding Site of an Insect GABA Receptor

(2011) S. C. R. Lummis et al.   JOURNAL OF NEUROSCIENCE

Principles of activation and permeation in an anion-selective Cys-loop receptor

(2011) Ryan E. Hibbs et al.   NATURE

New insights into the GABAA receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data

(2011) Tommy Sander et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Characterization of Agonists That Bind to an Insect GABA Receptor

(2010) Ian McGonigle et al.   BIOCHEMISTRY

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

(2010) Oliver F. Lange et al.   BIOPHYSICAL JOURNAL

Rapid desensitization of the rat α7 nAChR is facilitated by the presence of a proline residue in the outer β-sheet

(2010) Thomas J. McCormack et al.   JOURNAL OF PHYSIOLOGY-LONDON

Nicotinic pharmacophore: The pyridine N of nicotine and carbonyl of acetylcholine hydrogen bond across a subunit interface to a backbone NH

(2010) A. P. Blum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical potentials for fold assessment

(2010) Francisco Melo et al.   PROTEIN SCIENCE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

A prokaryotic perspective on pentameric ligand-gated ion channel structure

(2009) Ricarda JC Hilf et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Use of Acetylcholine Binding Protein in the Search for Novel α7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X-ray Analysis†

(2009) Chris Ulens et al.   JOURNAL OF MEDICINAL CHEMISTRY

Trans−cis Switching Mechanisms in Proline Analogues and Their Relevance for the Gating of the 5-HT3Receptor

(2009) Claudio Melis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations

(2009) Vanessa Leone et al.   PLoS Computational Biology

Molecular Dynamics Simulations of GABA Binding to the GABAC Receptor: The Role of Arg104

(2008) Claudio Melis et al.   BIOPHYSICAL JOURNAL

Cys-Loop Neuroreceptors: Structure to the Rescue?

(2008) Dennis A. Dougherty   CHEMICAL REVIEWS

Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel

(2008) Ricarda J. C. Hilf et al.   NATURE

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

(2008) Nicolas Bocquet et al.   NATURE

X-ray structure of a prokaryotic pentameric ligand-gated ion channel

(2008) Ricarda J. C. Hilf et al.   NATURE

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

QMEAN: A comprehensive scoring function for model quality assessment

(2007) Pascal Benkert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS