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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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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. |
format | Online Article Text |
id | pubmed-9825476 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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