2025 年的 GPCRdb:增加气味受体、数据映射器、结构相似性搜索和生理配体复合物模型。

IF 16.6 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-11-18 DOI:10.1093/nar/gkae1065
Luis P Taracena Herrera, Søren N Andreassen, Jimmy Caroli, Ismael Rodríguez-Espigares, Ali A Kermani, György M Keserű, Albert J Kooistra, Gáspár Pándy-Szekeres, David E Gloriam
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引用次数: 0

摘要

G 蛋白偶联受体(GPCR)是跨膜的传导体,可介导多种生理配体和药物的作用。GPCR 数据库 GPCRdb 在参考数据、分析、可视化、实验设计和传播方面为庞大的全球研究团体提供支持。在此,我们将从受体和配体的所有资源概述开始,介绍我们发布的第六个主要 GPCRdb 版本。作为一项重要补充,现在可以通过各种数据和工具资源对所有 400 多种人类气味受体及其在主要模式生物中的同源物进行研究。数据映射器页面首次允许用户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。结构模型数据增加了生理配体复合物模型,并更新了所有人类 GPCR 的新的特定状态结构模型(使用 AlphaFold、RoseTTAFold 和 AlphaFold-Multistate 构建)。此外,现在还可以通过实施 FoldSeek 的结构相似性(Structuresimilarity)搜索页面,对照 GPCRdb 的整个结构/模型集查询结构或模型(pdb 文件)。最后,对于配体,新的搜索工具可以根据 ChEMBL、Guide to Pharmacology、PDSP Ki、PubChem、DrugCentral 和 DrugBank 数据库中的整合条目查询名称、数据库标识符、相似性或子结构图。GPCRdb 可在 https://gpcrdb.org 上查阅。
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GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes.

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.

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来源期刊
Nucleic Acids Research
Nucleic Acids Research 生物-生化与分子生物学
CiteScore
27.10
自引率
4.70%
发文量
1057
审稿时长
2 months
期刊介绍: Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.
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