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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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

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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

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Use of the X-ray structure of the Beta2-adrenergic receptor for drug discovery

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Use of the X-ray structure of the β2-adrenergic receptor for drug discovery. Part 2: Identification of active compounds

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Docking-based virtual screening for ligands of G protein-coupled receptors: Not only crystal structures but also in silico models

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In silico analysis of the binding of agonists and blockers to the β2-adrenergic receptor

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

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

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

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Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation

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GPCR agonist binding revealed by modeling and crystallography

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Diversity and modularity of G protein-coupled receptor structures

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Structure-based drug screening for G-protein-coupled receptors

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[19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors

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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

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Identifying and Characterizing Binding Sites and Assessing Druggability

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

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Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

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

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Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

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Modeling Water Molecules in Protein−Ligand Docking Using GOLD

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Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

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Structure-Based Discovery of A 2A Adenosine Receptor Ligands

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

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

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Structure-Based Discovery of Novel Chemotypes for Adenosine A2AReceptor Antagonists

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Crystal structure of the ligand-free G-protein-coupled receptor opsin

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

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Crystal structure of opsin in its G-protein-interacting conformation

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Structure of a nanobody-stabilized active state of the β2 adrenoceptor

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The structural basis for agonist and partial agonist action on a β1-adrenergic receptor

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Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation

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Crystal structure of the β2 adrenergic receptor–Gs protein complex

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

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Structure and dynamics of the M3 muscarinic acetylcholine receptor

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

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Structure-based discovery of β 2 -adrenergic receptor ligands

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

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

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The second extracellular loop of the dopamine D 2 receptor lines the binding-site crevice

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Clustal W and Clustal X version 2.0

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

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

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Structure of an Agonist-Bound Human A 2A Adenosine Receptor

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Crystal Structure of a Lipid G Protein–Coupled Receptor

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Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor

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Structure of the human kappa opioid receptor in complex with JDTic

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.70675/c1795a76z5609z441dz9f37zffff967bbb4fopenalex-snapshot

Études par dynamique moléculaire de l’interaction de Récepteurs Couplés aux Protéines-G avec leurs partenaires extra et intra-cellulaires

inferred← citeshttps://doi.org/10.7554/elife.112734openalex-snapshot

Distal conformational steering by N-terminal pyroglutamylation enables subtype-selective GPCR activation across Aplysia PRXamide and human Neuromedin U signaling

inferred← citeshttps://doi.org/10.7554/elife.112734.1openalex-snapshot

Distal conformational steering by N-terminal pyroglutamylation enables subtype-selective GPCR activation across Aplysia PRXamide and human Neuromedin U signaling

inferred← citeshttps://doi.org/10.7554/elife.89386openalex-snapshot

How accurately can one predict drug binding modes using AlphaFold models?

inferred← citeshttps://doi.org/10.7554/elife.89386.1openalex-snapshot

How accurately can one predict drug binding modes using AlphaFold models?

inferred← citeshttps://doi.org/10.7554/elife.89386.2openalex-snapshot

How accurately can one predict drug binding modes using AlphaFold models?

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