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2025年的GPCRdb:增加嗅觉受体、数据映射器、结构相似性搜索和生理性配体复合物模型。

GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes.

作者信息

Herrera Luis P Taracena, Andreassen Søren N, Caroli Jimmy, Rodríguez-Espigares Ismael, Kermani Ali A, Keserű György M, Kooistra Albert J, Pándy-Szekeres Gáspár, Gloriam David E

机构信息

Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.

Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA.

出版信息

Nucleic Acids Res. 2025 Jan 6;53(D1):D425-D435. doi: 10.1093/nar/gkae1065.

Abstract

G protein-coupled receptors (GPCRs) are membrane-spanning transducers mediating the actions of numerous physiological ligands and drugs. The GPCR database GPCRdb supports a large global research community with reference data, analysis, visualization, experiment design and dissemination. Here, we describe our sixth major GPCRdb release starting with an overview of all resources for receptors and ligands. As a major addition, all ∼400 human odorant receptors and their orthologs in major model organisms can now be studied across the various data and tool resources. For the first time, a Data mapper page enables users to map their own data onto receptors visualized as a GPCRome wheel, tree, clusters, list or heatmap. The structure model data have been expanded with models of physiological ligand complexes and updated with new state-specific structure models of all human GPCRs (built using AlphaFold, RoseTTAFold and AlphaFold-Multistate). Furthermore, a structure or model (pdb file) can now be queried against GPCRdb's entire structure/model collection through a Structuresimilarity search page implementing FoldSeek. Finally, for ligands, new search tools can query names, database identifiers, similarities or substructures against integrated entries from the ChEMBL, Guide to Pharmacology, PDSP Ki, PubChem, DrugCentral and DrugBank databases. GPCRdb is available at https://gpcrdb.org.

摘要

G蛋白偶联受体(GPCRs)是跨膜转导蛋白,介导众多生理配体和药物的作用。GPCR数据库GPCRdb为全球大型研究群体提供参考数据、分析、可视化、实验设计及传播等支持。在此,我们介绍GPCRdb的第六次重大发布,首先概述受体和配体的所有资源。作为一项主要新增内容,现在可以通过各种数据和工具资源研究所有约400种人类嗅觉受体及其在主要模式生物中的直系同源物。首次推出的数据映射器页面使用户能够将自己的数据映射到可视化为GPCRome轮、树、簇、列表或热图的受体上。结构模型数据已通过生理配体复合物模型进行扩展,并使用所有人类GPCR的新的状态特异性结构模型(使用AlphaFold、RoseTTAFold和AlphaFold-Multistate构建)进行了更新。此外,现在可以通过实施FoldSeek的结构相似性搜索页面,针对GPCRdb的整个结构/模型集合查询结构或模型(pdb文件)。最后,对于配体,新的搜索工具可以根据来自ChEMBL、《药理学指南》、PDSP Ki、PubChem、DrugCentral和DrugBank数据库的综合条目查询名称、数据库标识符、相似性或子结构。可通过https://gpcrdb.org访问GPCRdb。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d162/11701689/601435e4195d/gkae1065figgra1.jpg

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