- GPCRdb: an information system for G protein-coupled receptors. [PMID: 26582914]
Vignir Isberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S Hauser, Bas Vroling, Andrzej J Bojarski, Gert Vriend, David E Gloriam
Nucleic acids research 2016:44(D1)
1 Citations (Google Scholar as of 2016-01-29)
Abstract: Recent developments in G protein-coupled receptor (GPCR) structural biology and pharmacology have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing reference data, analysis tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iii) phylogenetic trees with receptor classification colour schemes. Under the hood, the entire GPCRdb front- and back-ends have been re-coded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
- GPCRDB: an information system for G protein-coupled receptors. [PMID: 24304901]
Vignir Isberg, Bas Vroling, Rob van der Kant, Kang Li, Gert Vriend, David Gloriam
Nucleic acids research 2014:42(Database issue)
41 Citations (Google Scholar as of 2016-01-23)
Abstract: 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.
- GPCRDB: information system for G protein-coupled receptors. [PMID: 21045054]
Bas Vroling, Marijn Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend
Nucleic acids research 2011:39(Database issue)
128 Citations (Google Scholar as of 2016-01-23)
Abstract: The GPCRDB is a Molecular Class-Specific Information System (MCSIS) that collects, combines, validates and disseminates large amounts of heterogeneous data on G protein-coupled receptors (GPCRs). 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 provides access to the data via a number of different access methods. It offers visualization and analysis tools, and a number of query systems. The data is updated automatically on a monthly basis. The GPCRDB can be found online at http://www.gpcr.org/7tm/.
- GPCRDB information system for G protein-coupled receptors. [PMID: 12520006]
Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E Cohen, Gerrit Vriend
Nucleic acids research 2003:31(1)
382 Citations (Google Scholar as of 2016-01-23)
Abstract: The GPCRDB is a molecular class-specific information system that collects, combines, validates and disseminates heterogeneous data on G protein-coupled receptors (GPCRs). The database stores data on sequences, ligand binding constants and mutations. The system also provides computationally derived data such as sequence alignments, homology models, and a series of query and visualization tools. The GPCRDB is updated automatically once every 4-5 months and is freely accessible at http://www.gpcr.org/7tm/.
- GPCRDB: an information system for G protein-coupled receptors. [PMID: 9399852]
F Horn, J Weare, M W Beukers, S Hörsch, A Bairoch, W Chen, O Edvardsen, F Campagne, G Vriend
Nucleic acids research 1998:26(1)
412 Citations (Google Scholar as of 2016-01-23)
Abstract: The GPCRDB is a G protein-coupled receptor (GPCR) database system aimed at the collection and dissemination of GPCR related data. It holds sequences, mutant data and ligand binding constants as primary (experimental) data. Computationally derived data such as multiple sequence alignments, three dimensional models, phylogenetic trees and two dimensional visualization tools are added to enhance the database's usefulness. The GPCRDB is an EU sponsored project aimed at building a generic molecular class specific database capable of dealing with highly heterogeneous data. GPCRs were chosen as test molecules because of their enormous importance for medical sciences and due to the availability of so much highly heterogeneous data. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm