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GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources

G protein-coupled receptors (GPCRs) are physiologically abundant signaling hubs routing hundreds of extracellular signal substances and drugs into intracellular pathways. The GPCR database, GPCRdb supports >5000 interdisciplinary researchers every month with reference data, analysis, visualizatio...

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Autores principales: Pándy-Szekeres, Gáspár, Caroli, Jimmy, Mamyrbekov, Alibek, Kermani, Ali A, Keserű, György M, Kooistra, Albert J, Gloriam, David E
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825476/
https://www.ncbi.nlm.nih.gov/pubmed/36395823
http://dx.doi.org/10.1093/nar/gkac1013
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author Pándy-Szekeres, Gáspár
Caroli, Jimmy
Mamyrbekov, Alibek
Kermani, Ali A
Keserű, György M
Kooistra, Albert J
Gloriam, David E
author_facet Pándy-Szekeres, Gáspár
Caroli, Jimmy
Mamyrbekov, Alibek
Kermani, Ali A
Keserű, György M
Kooistra, Albert J
Gloriam, David E
author_sort Pándy-Szekeres, Gáspár
collection PubMed
description G protein-coupled receptors (GPCRs) are physiologically abundant signaling hubs routing hundreds of extracellular signal substances and drugs into intracellular pathways. The GPCR database, GPCRdb supports >5000 interdisciplinary researchers every month with reference data, analysis, visualization, experiment design and dissemination. Here, we present our fifth major GPCRdb release setting out with an overview of the many resources for receptor sequences, structures, and ligands. This includes recently published additions of class D generic residue numbers, a comparative structure analysis tool to identify functional determinants, trees clustering GPCR structures by 3D conformation, and mutations stabilizing inactive/active states. We provide new state-specific structure models of all human non-olfactory GPCRs built using AlphaFold2-MultiState. We also provide a new resource of endogenous ligands along with a larger number of surrogate ligands with bioactivity, vendor, and physiochemical descriptor data. The one-stop-shop ligand resources integrate ligands/data from the ChEMBL, Guide to Pharmacology, PDSP Ki and PubChem database. The GPCRdb is available at https://gpcrdb.org.
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spelling pubmed-98254762023-01-10 GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources Pándy-Szekeres, Gáspár Caroli, Jimmy Mamyrbekov, Alibek Kermani, Ali A Keserű, György M Kooistra, Albert J Gloriam, David E Nucleic Acids Res Database Issue G protein-coupled receptors (GPCRs) are physiologically abundant signaling hubs routing hundreds of extracellular signal substances and drugs into intracellular pathways. The GPCR database, GPCRdb supports >5000 interdisciplinary researchers every month with reference data, analysis, visualization, experiment design and dissemination. Here, we present our fifth major GPCRdb release setting out with an overview of the many resources for receptor sequences, structures, and ligands. This includes recently published additions of class D generic residue numbers, a comparative structure analysis tool to identify functional determinants, trees clustering GPCR structures by 3D conformation, and mutations stabilizing inactive/active states. We provide new state-specific structure models of all human non-olfactory GPCRs built using AlphaFold2-MultiState. We also provide a new resource of endogenous ligands along with a larger number of surrogate ligands with bioactivity, vendor, and physiochemical descriptor data. The one-stop-shop ligand resources integrate ligands/data from the ChEMBL, Guide to Pharmacology, PDSP Ki and PubChem database. The GPCRdb is available at https://gpcrdb.org. Oxford University Press 2022-11-18 /pmc/articles/PMC9825476/ /pubmed/36395823 http://dx.doi.org/10.1093/nar/gkac1013 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Pándy-Szekeres, Gáspár
Caroli, Jimmy
Mamyrbekov, Alibek
Kermani, Ali A
Keserű, György M
Kooistra, Albert J
Gloriam, David E
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
title GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
title_full GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
title_fullStr GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
title_full_unstemmed GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
title_short GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
title_sort gpcrdb in 2023: state-specific structure models using alphafold2 and new ligand resources
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825476/
https://www.ncbi.nlm.nih.gov/pubmed/36395823
http://dx.doi.org/10.1093/nar/gkac1013
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