Towards predictive docking at aminergic G-protein coupled receptors

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

(2015) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands

(2014) Ádám A. Kelemen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular dynamics simulations to explore the active/inactive conformers of guinea pig β2adrenoceptor for the selective design of agonists or antagonists

(2014) A. Segura-Cabrera et al.   MOLECULAR SIMULATION

Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges

(2014) Irina Kufareva et al.   STRUCTURE

Homology Modeling of Human Muscarinic Acetylcholine Receptors

(2013) Trayder Thomas et al.   Journal of Chemical Information and Modeling

Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR–Ligand Recognition: The Human A2A Adenosine Receptor as a Key Study

(2013) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

(2013) Kai Wang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation

(2013) James S. Wright et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular interactions between fenoterol stereoisomers and derivatives and the β2-adrenergic receptor binding site studied by docking and molecular dynamics simulations

(2013) Anita Plazinska et al.   JOURNAL OF MOLECULAR MODELING

Essential considerations for using protein–ligand structures in drug discovery

(2012) Gregory L. Warren et al.   DRUG DISCOVERY TODAY

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines

(2012) Thijs Beuming et al.   Journal of Chemical Information and Modeling

Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist

(2012) Kazuko Haga et al.   NATURE

Structure and dynamics of the M3 muscarinic acetylcholine receptor

(2012) Andrew C. Kruse et al.   NATURE

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

(2012) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G Protein- and Agonist-Bound Serotonin 5-HT2AReceptor Model Activated by Steered Molecular Dynamics Simulations

(2011) Vignir Ísberg et al.   Journal of Chemical Information and Modeling

In Silico screening for agonists and blockers of the β2 adrenergic receptor: Implications of inactive and activated state structures

(2011) Stefano Costanzi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Role of Conformational Ensembles in Ligand Recognition in G-Protein Coupled Receptors

(2011) Michiel J. M. Niesen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure of the human histamine H1 receptor complex with doxepin

(2011) Tatsuro Shimamura et al.   NATURE

Two distinct conformations of helix 6 observed in antagonist-bound structures of a  1-adrenergic receptor

(2011) R. Moukhametzianov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Progress in the structural prediction of G protein-coupled receptors: D3 receptor in complex with eticlopride

(2011) Cristian Obiol-Pardo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment

(2011) Irina Kufareva et al.   STRUCTURE

Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors

(2010) Fiona M. McRobb et al.   Journal of Chemical Information and Modeling

Conserved Binding Mode of Human β2Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

(2010) Daniel Wacker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist

(2010) E. Y. T. Chien et al.   SCIENCE

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

(2009) Mayako Michino et al.   NATURE REVIEWS DRUG DISCOVERY

Selective Structure-Based Virtual Screening for Full and Partial Agonists of the β2 Adrenergic Receptor

(2008) Chris de Graaf et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure of a β1-adrenergic G-protein-coupled receptor

(2008) Tony Warne et al.   NATURE

A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor

(2008) Michael A. Hanson et al.   STRUCTURE