Feng Yue, Qaseem Ammar, Moumbock Aurélien F A, Pan Shuling, Kirchner Pascal A, Simoben Conrad V, Malange Yvette I, Babiaka Smith B, Gao Mingjie, Günther Stefan
Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany.
Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.
Nucleic Acids Res. 2025 Jan 6;53(D1):D724-D729. doi: 10.1093/nar/gkae1030.
Streptomycetes remain an important bacterial source of natural products (NPs) with significant therapeutic promise, particularly in the fight against antimicrobial resistance. Herein, we present StreptomeDB 4.0, a substantial update of the database that includes expanded content and several new features. Currently, StreptomeDB 4.0 contains over 8500 NPs originating from ∼3900 streptomycetes, manually annotated from ∼7600 PubMed-indexed peer-reviewed articles. The database was enhanced by two in-house developments: (i) automated literature-mined NP-protein relationships (hyperlinked to the CPRiL web server) and (ii) pharmacophore-based NP-protein interactions (predicted with the ePharmaLib dataset). Moreover, genome mining was supplemented through hyperlinks to the widely used antiSMASH database. To facilitate NP structural dereplication, interactive visualization tools were implemented, namely the JSpecView applet and plotly.js charting library for predicted nuclear magnetic resonance and mass spectrometry spectral data, respectively. Furthermore, both the backend database and the frontend web interface were redesigned, and several software packages, including PostgreSQL and Django, were updated to the latest versions. Overall, this comprehensive database serves as a vital resource for researchers seeking to delve into the metabolic intricacies of streptomycetes and discover novel therapeutics, notably antimicrobial agents. StreptomeDB is publicly accessible at https://www.pharmbioinf.uni-freiburg.de/streptomedb.
链霉菌仍然是具有重大治疗前景的天然产物的重要细菌来源，尤其是在对抗抗菌药物耐药性方面。在此，我们展示了链霉菌数据库（StreptomeDB）4.0，这是该数据库的一次重大更新，包括内容扩展和几个新功能。目前，链霉菌数据库4.0包含来自约3900种链霉菌的8500多种天然产物，这些产物是从约7600篇被PubMed索引的同行评审文章中手动注释而来的。该数据库通过两项内部开发得到了增强：（i）自动从文献中挖掘的天然产物-蛋白质关系（超链接到CPRiL网络服务器）和（ii）基于药效团的天然产物-蛋白质相互作用（使用ePharmaLib数据集进行预测）。此外，通过超链接到广泛使用的antiSMASH数据库对基因组挖掘进行了补充。为了便于天然产物的结构去重复，实现了交互式可视化工具，即分别用于预测核磁共振和质谱光谱数据的JSpecView小程序和plotly.js图表库。此外，对后端数据库和前端网页界面都进行了重新设计，并且将包括PostgreSQL和Django在内的几个软件包更新到了最新版本。总体而言，这个综合数据库是研究人员探索链霉菌代谢复杂性和发现新型治疗药物（尤其是抗菌剂）的重要资源。链霉菌数据库可通过https://www.pharmbioinf.uni-freiburg.de/streptomedb公开访问。
