Protein-based virtual screening of chemical databases. II. Are homology models of g-protein coupled receptors suitable targets?

2002 ◽  
Vol 50 (1) ◽  
pp. 5-25 ◽  
Author(s):  
Caterina Bissantz ◽  
Philippe Bernard ◽  
Marcel Hibert ◽  
Didier Rognan
Keyword(s):  
Virtual Screening ◽  
G Protein ◽  
G Protein Coupled Receptors ◽  
Chemical Databases ◽  
G Protein Coupled ◽  
Homology Models

scholarly journals Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You?

2021 ◽  
Vol 73 (4) ◽  
pp. 527-565
Author(s):  
Flavio Ballante ◽  
Albert J Kooistra ◽  
Stefanie Kampen ◽  
Chris de Graaf ◽  
Jens Carlsson
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
G Protein ◽  
G Protein Coupled Receptors ◽  
G Protein Coupled

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

MedChemComm ◽  
2015 ◽  
Vol 6 (6) ◽  
pp. 1003-1017 ◽  
Author(s):  
Enade P. Istyastono ◽  
Albert J. Kooistra ◽  
Henry F. Vischer ◽  
Martien Kuijer ◽  
Luc Roumen ◽  
...  
Keyword(s):  
Virtual Screening ◽  
G Protein ◽  
Histamine H4 Receptor ◽  
H4 Receptor ◽  
G Protein Coupled ◽  
Homology Models

Structure-based virtual screening using H1R- and β2R-based histamine H4R homology models identified 9 fragments with an affinity ranging from 0.14 to 6.3 μm for H4R.

scholarly journals Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation

2018 ◽  
Author(s):  
Ashley R. Vidad ◽  
Stephen Macaspac ◽  
Ho-Leung Ng
Keyword(s):  
Ligand Binding ◽  
G Protein ◽  
Binding Sites ◽  
G Protein Coupled Receptors ◽  
Sequence Conservation ◽  
Surface Geometry ◽  
A2a Adenosine Receptors ◽  
Ligand Binding Sites ◽  
G Protein Coupled ◽  
Homology Models

AbstractG-protein coupled receptors (GPCRs) are the largest protein family of drug targets. Detailed mechanisms of binding are unknown for many important GPCR-ligand pairs due to the difficulties of GPCR recombinant expression, biochemistry, and crystallography. We describe our new method, ConDock, for predicting ligand binding sites in GPCRs using combined information from surface conservation and docking starting from crystal structures or homology models. We demonstrate the effectiveness of ConDock on well-characterized GPCRs such as the β2 adrenergic and A2A adenosine receptors. We also demonstrate that ConDock successfully predicts ligand binding sites from high-quality homology models. Finally, we apply ConDock to predict ligand binding sites on a structurally uncharacterized GPCR, GPER. GPER is the G-protein coupled estrogen receptor, with four known ligands: estradiol, G1, G15, and tamoxifen. ConDock predicts that all four ligands bind to the same location on GPER, centered on L119, H307, and N310; this site is deeper in the receptor cleft than predicted by previous studies. We compare the sites predicted by ConDock and traditional methods that utilize information from surface geometry, surface conservation, and ligand chemical interactions. Incorporating sequence conservation information in ConDock overcomes errors introduced from physics-based scoring functions and homology modeling.

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

2011 ◽  
Vol 29 (5) ◽  
pp. 614-623 ◽  
Author(s):  
Santiago Vilar ◽  
Giulio Ferino ◽  
Sharangdhar S. Phatak ◽  
Barkin Berk ◽  
Claudio N. Cavasotto ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Crystal Structures ◽  
G Protein ◽  
In Silico ◽  
G Protein Coupled Receptors ◽  
In Silico Models ◽  
G Protein Coupled

scholarly journals Critical analysis of the successes and failures of homology models of G protein-coupled receptors

2013 ◽  
Vol 81 (5) ◽  
pp. 729-739 ◽  
Author(s):  
Supriyo Bhattacharya ◽  
Alfonso Ramon Lam ◽  
Hubert Li ◽  
Gouthaman Balaraman ◽  
Michiel Jacobus Maria Niesen ◽  
...  
Keyword(s):  
G Protein ◽  
Critical Analysis ◽  
G Protein Coupled Receptors ◽  
G Protein Coupled ◽  
Homology Models ◽  
Successes And Failures
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