StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization.

IF 16.6 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yue Feng, Ammar Qaseem, Aurélien F A Moumbock, Shuling Pan, Pascal A Kirchner, Conrad V Simoben, Yvette I Malange, Smith B Babiaka, Mingjie Gao, Stefan Günther
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引用次数: 0

Abstract

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.

StreptomeDB 4.0:链霉菌天然产品综合数据库,富含蛋白质相互作用和交互式光谱可视化。
链霉菌仍然是天然产物(NPs)的重要细菌来源,具有重要的治疗前景,尤其是在对抗抗菌药耐药性方面。在此,我们介绍 StreptomeDB 4.0,这是对数据库的一次重大更新,包括扩展内容和一些新功能。目前,StreptomeDB 4.0 包含来自 3900 ∼3900 种链霉菌的 8500 多个 NPs,这些 NPs 都是从 7600 ∼7600 篇 PubMed 索引的同行评审文章中人工标注的。该数据库通过两项内部开发得到了增强:(i) 自动文献挖掘 NP 蛋白关系(超链接到 CPRiL 网络服务器)和 (ii) 基于药理的 NP 蛋白相互作用(利用 ePharmaLib 数据集预测)。此外,通过与广泛使用的 antiSMASH 数据库的超链接,对基因组挖掘进行了补充。为促进核蛋白结构的去重,还实施了交互式可视化工具,即 JSpecView applet 和 plotly.js 图表库,分别用于预测核磁共振和质谱光谱数据。此外,还重新设计了后台数据库和前台网页界面,并将 PostgreSQL 和 Django 等多个软件包更新到最新版本。总之,这个全面的数据库是研究人员深入研究链霉菌复杂的新陈代谢和发现新型疗法(特别是抗菌剂)的重要资源。StreptomeDB 可通过 https://www.pharmbioinf.uni-freiburg.de/streptomedb 公开访问。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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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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