Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

Structures of the 5-HT2A receptor in complex with the antipsychotics risperidone and zotepine

(2019) Kanako Terakado Kimura et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

The Molecular Basis of G Protein–Coupled Receptor Activation

(2018) William I. Weis et al.   Annual Review of Biochemistry

5-HT 2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology

(2018) Yao Peng et al.   CELL

Selectivity Challenges in Docking Screens for GPCR Targets and Anti-Targets

(2018) Dahlia R Weiss et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone

(2018) Sheng Wang et al.   NATURE

A benchmarking study on virtual ligand screening against homology models of human GPCRs

(2018) Victor Jun Yu Lim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries

(2018) Thibault Tubiana et al.   Journal of Chemical Information and Modeling

Aminergic GPCR–Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data

(2018) Márton Vass et al.   JOURNAL OF MEDICINAL CHEMISTRY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Trends in GPCR drug discovery: new agents, targets and indications

(2017) Alexander S. Hauser et al.   NATURE REVIEWS DRUG DISCOVERY

GPCRdb in 2018: adding GPCR structure models and ligands

(2017) Gáspár Pándy-Szekeres et al.   NUCLEIC ACIDS RESEARCH

What makes it difficult to refine protein models further via molecular dynamics simulations?

(2017) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

D4dopamine receptor high-resolution structures enable the discovery of selective agonists

(2017) Sheng Wang et al.   SCIENCE

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

Novel and High Affinity 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues as Atypical Dopamine Transporter Inhibitors

(2016) Jianjing Cao et al.   JOURNAL OF MEDICINAL CHEMISTRY

High-resolution crystal structure of the human CB1 cannabinoid receptor

(2016) Zhenhua Shao et al.   NATURE

Crystal structures of the M1 and M4 muscarinic acetylcholine receptors

(2016) David M. Thal et al.   NATURE

Structure-based discovery of opioid analgesics with reduced side effects

(2016) Aashish Manglik et al.   NATURE

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models

(2015) Anirudh Ranganathan et al.   JOURNAL OF MEDICINAL CHEMISTRY

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(2015) Xi-Ping Huang et al.   NATURE

Discovery of trace amine-associated receptor 1 ligands by molecular docking screening against a homology model

(2015) V. M. Lam et al.   MedChemComm

Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4 receptor

(2015) Enade P. Istyastono et al.   MedChemComm

Virtual fragment screening on GPCRs: A case study on dopamine D3 and histamine H4 receptors

(2014) Márton Vass et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Strategies for Improved Modeling of GPCR-Drug Complexes: Blind Predictions of Serotonin Receptors Bound to Ergotamine

(2014) David Rodríguez et al.   Journal of Chemical Information and Modeling

Impact of Template Choice on Homology Model Efficiency in Virtual Screening

(2014) Krzysztof Rataj et al.   Journal of Chemical Information and Modeling

Structure-Based Discovery of Selective Serotonin 5-HT 1B Receptor Ligands

(2014) David Rodríguez et al.   STRUCTURE

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

(2014) Irina Kufareva et al.   STRUCTURE

Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor

(2013) Dahlia R. Weiss et al.   ACS Chemical Biology

Ligand-Optimized Homology Models of D1 and D2 Dopamine Receptors: Application for Virtual Screening

(2013) Marcin Kołaczkowski et al.   Journal of Chemical Information and Modeling

The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs

(2013) Ákos Tarcsay et al.   Journal of Chemical Information and Modeling

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Structural Basis for Molecular Recognition at Serotonin Receptors

(2013) C. Wang et al.   SCIENCE

Structural Features for Functional Selectivity at Serotonin Receptors

(2013) D. Wacker et al.   SCIENCE

Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints

(2012) Francesco Sirci et al.   Journal of Chemical Information and Modeling

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

(2012) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4

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Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H1Receptor

(2011) Chris de Graaf et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure of the human histamine H1 receptor complex with doxepin

(2011) Tatsuro Shimamura et al.   NATURE

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

(2011) Jens Carlsson et al.   Nature Chemical Biology

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Irina Kufareva et al.   STRUCTURE

Ligand-Steered Modeling and Docking: A Benchmarking Study in Class A G-Protein-Coupled Receptors

(2010) Sharangdhar S. Phatak et al.   Journal of Chemical Information and Modeling

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

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

Rapid Context-Dependent Ligand Desolvation in Molecular Docking

(2010) Michael M. Mysinger et al.   Journal of Chemical Information and Modeling

Structure-Based Discovery of A2AAdenosine Receptor Ligands

(2010) Jens Carlsson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure based prediction of subtype-selectivity for adenosine receptor antagonists

(2010) Vsevolod Katritch et al.   NEUROPHARMACOLOGY

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

Molecular Docking Screens Using Comparative Models of Proteins

(2009) Hao Fan et al.   Journal of Chemical Information and Modeling

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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

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

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

Structure-based discovery of  2-adrenergic receptor ligands

(2009) P. Kolb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL 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

Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening

(2007) Chris de Graaf et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS