Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

Molecular sampling of the allosteric binding pocket of the TSH receptor provides discriminative pharmacophores for antagonist and agonists

(2013) Inna Hoyer et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The Dynamic Process of β2-Adrenergic Receptor Activation

(2013) Rie Nygaard et al.   CELL

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

Fragment Based Drug Design: From Experimental to Computational Approaches

(2012) A. Kumar et al.   CURRENT MEDICINAL CHEMISTRY

Computational Tools for In Silico Fragment-Based Drug Design

(2012) Jeremie Mortier et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Identification of Critical Residues Involved in Ligand Binding and G Protein Signaling in Human Somatostatin Receptor Subtype 2

(2012) Jesse J. Parry et al.   ENDOCRINOLOGY

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

Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge

(2012) Ashutosh Kumar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure of the δ-opioid receptor bound to naltrindole

(2012) Sébastien Granier et al.   NATURE

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

(2012) Kazuko Haga et al.   NATURE

Structure of the human κ-opioid receptor in complex with JDTic

(2012) Huixian Wu et al.   NATURE

Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic

(2012) Aaron A. Thompson et al.   NATURE

Crystal structure of the µ-opioid receptor bound to a morphinan antagonist

(2012) Aashish Manglik et al.   NATURE

Structure and dynamics of the M3 muscarinic acetylcholine receptor

(2012) Andrew C. Kruse et al.   NATURE

Using RosettaLigand for Small Molecule Docking into Comparative Models

(2012) Kristian W. Kaufmann et al.   PLoS One

Naturally evolved G protein-coupled receptors adopt metastable conformations

(2012) K.-Y. M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structure of a Lipid G Protein-Coupled Receptor

(2012) M. A. Hanson et al.   SCIENCE

GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models

(2011) Catherine L Worth et al.   BMC BIOINFORMATICS

Structure of the human histamine H1 receptor complex with doxepin

(2011) Tatsuro Shimamura et al.   NATURE

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors

(2011) D. A. Goldfeld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Irina Kufareva et al.   STRUCTURE

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts

(2010) M. Rueda et al.   BIOINFORMATICS

LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops

(2010) Paul Labute   Journal of Chemical Information and Modeling

Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists

(2010) B. Wu et al.   SCIENCE

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

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

ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments

(2009) Charles Simon Bond et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use?

(2009) Juan Carlos Mobarec et al.   JOURNAL OF MEDICINAL CHEMISTRY

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

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

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

Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors

(2009) Gregory V. Nikiforovich et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

(2008) Giovanni Bottegoni et al.   JOURNAL OF MEDICINAL CHEMISTRY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2008) Tony Warne et al.   NATURE

Structural diversity of G protein-coupled receptors and significance for drug discovery

(2008) Malin C. Lagerström et al.   NATURE REVIEWS DRUG DISCOVERY

The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist

(2008) V.-P. Jaakola et al.   SCIENCE