GPCRDB: an information system for G protein-coupled receptors

By Vignir Ísberg, B. Vroling, R. V. D. Kant, Kang Li, G. Vriend, David E. Gloriam. 2013

507 citations recorded by the source corpus.

For the past 20 years, the GPCRDB (G protein-coupled receptors database; http://www.gpcr.org/7tm/) has been a ‘one-stop shop’ for G protein-coupled receptor (GPCR)-related data. The GPCRDB contains experimental data on sequences, ligand-binding constants, mutations and oligomers, as well as many different types of computationally derived data, such as multiple sequence alignments and homology models. The GPCRDB also provides visualization and analysis tools, plus a number of query systems. In the latest GPCRDB release, all multiple sequence alignments, and >65 000 homology models, have been significantly improved, thanks to a recent flurry of GPCR X-ray structure data. Tools were introduced to browse X-ray structures, compare binding sites, profile similar receptors and generate amino acid conservation statistics. Snake plots and helix box diagrams can now be custom coloured (e.g. by chemical properties or mutation data) and saved as figures. A series of sequence alignment visualization tools has been added, and sequence alignments can now be created for subsets of sequences and sequence positions, and alignment statistics can be produced for any of these subsets.

Subfields: Cellular and Molecular Neuroscience, Molecular Biology, Surgery

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Citations in the corpus

ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “BRENDA provides binding constants for enzymes (14), IUPHAR contains ligand information for receptors and ion channels (15), while GLIDA (16) and GPCRDB (17) provide information speciﬁcally for G-protein-coupled receptors.”
Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, methodology): “First, alignments were extracted from GPCRdb.”
The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, methodology): “PMP relies on models provided by several research groups such as Center for Structures of Proteins in Membranes (CSMP) (12), North Eastern Structural Genomics Center (NESG) (13), New York Structural Genomics Research Consortium (NYSGRC) (14), ModBase (15), SWISS-MODEL Repository (16) and GPCRDB (17)”
A series of PDB-related databanks for everyday needs (2014, methodology): “We developed the visualization tool VASE (Visualization of Alignments, Structure and Entropy) (50) that connects the three components structure, alignment and entropy/variability in a single browser window.”
GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors (2016, background): “currently being used for research and teaching purposes in several institutions worldwide (11,12) and it has been considered in reviews of the field (13,14), as well as recently linked as an external tool to the reference database in the field, the GPCRdb (15).”
How accurately can one predict drug binding modes using AlphaFold models? (2023, methodology): “We selected structures from the aggregated list of all experimentally determined human GPCR structures from GPCRdb ( Isberg et al., 2014 ).”
A Structural Framework for GPCR Chemogenomics: What's In a Residue Number? (2018, methodology): “Such alignments are currently easily available in an interactive manner in GPCRdb [66, 67].”
5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology (2018, unknown): “ERG Binding Target Profiling The class A GPCR ERG target profiling was performed using a manual site search in the GPCRdb (Isberg et al., 2016) searching all receptors of the class for specific amino acids in the positions determined to be important for ERG binding in our structure- and sequence-bas”
GPCRdb: the G protein‐coupled receptor database – an introduction (2016, methodology): “The GPCR database, GPCRdb, is well-established in the GPCR community with more than 20 years of service and over a thousand citations (Horn et al., 1998; Horn et al., 2003; Vroling et al., 2011; Isberg et al., 2014, 2016).”
GPCRdb: an information system for G protein-coupled receptors (2015, methodology): “In 2013, the stewardship of GPCRdb was transferred to the David Gloriam group at the University of Copenhagen, backed up by an international team from the EU COST Action ‘GLISTEN’ (21).”
GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors (2017, methodology): “The sequences were downloaded from the GPCRdb in June 2016 (13).”