GPCRDB: an information system for G protein-coupled receptors

TY - JOUR

T1 - GPCRDB

T2 - an information system for G protein-coupled receptors

AU - Ísberg, Vignir

AU - Vroling, Bas

AU - van der Kant, Rob

AU - Li, Kang

AU - Vriend, Gert

AU - Gloriam, David

N1 - Funding: Lundbeck Foundation [R54-A5441 to V.I.]; the Carlsberg Foundation [R77-A6854 to D.G.] and the European Union NewProt project [289350 to G.V.]. Funding for open access charge: The publication was paid by the CMBI running costs.

PY - 2014/1/1

Y1 - 2014/1/1

N2 - 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.

AB - 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.

KW - Binding Sites

KW - Databases, Protein

KW - Internet

KW - Receptors, G-Protein-Coupled

KW - Sequence Alignment

KW - Sequence Analysis, Protein

KW - Software

KW - Structural Homology, Protein

U2 - 10.1093/nar/gkt1255

DO - 10.1093/nar/gkt1255

M3 - Journal article

C2 - 24304901

SN - 0305-1048

VL - 42

SP - D422-D425

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -