Szklarczyk Damian, Nastou Katerina, Koutrouli Mikaela, Kirsch Rebecca, Mehryary Farrokh, Hachilif Radja, Hu Dewei, Peluso Matteo E, Huang Qingyao, Fang Tao, Doncheva Nadezhda T, Pyysalo Sampo, Bork Peer, Jensen Lars J, von Mering Christian
Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
SIB Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland.
Nucleic Acids Res. 2025 Jan 6;53(D1):D730-D737. doi: 10.1093/nar/gkae1113.
Proteins cooperate, regulate and bind each other to achieve their functions. Understanding the complex network of their interactions is essential for a systems-level description of cellular processes. The STRING database compiles, scores and integrates protein-protein association information drawn from experimental assays, computational predictions and prior knowledge. Its goal is to create comprehensive and objective global networks that encompass both physical and functional interactions. Additionally, STRING provides supplementary tools such as network clustering and pathway enrichment analysis. The latest version, STRING 12.5, introduces a new 'regulatory network', for which it gathers evidence on the type and directionality of interactions using curated pathway databases and a fine-tuned language model parsing the literature. This update enables users to visualize and access three distinct network types-functional, physical and regulatory-separately, each applicable to distinct research needs. In addition, the pathway enrichment detection functionality has been updated, with better false discovery rate corrections, redundancy filtering and improved visual displays. The resource now also offers improved annotations of clustered networks and provides users with downloadable network embeddings, which facilitate the use of STRING networks in machine learning and allow cross-species transfer of protein information. The STRING database is available online at https://string-db.org/.
蛋白质相互协作、调节并结合以实现其功能。理解它们相互作用的复杂网络对于从系统层面描述细胞过程至关重要。STRING数据库汇编、评分并整合了来自实验分析、计算预测和先验知识的蛋白质-蛋白质关联信息。其目标是创建涵盖物理和功能相互作用的全面且客观的全球网络。此外，STRING还提供网络聚类和通路富集分析等补充工具。最新版本STRING 12.5引入了一个新的“调控网络”，为此它使用经过整理的通路数据库和经过微调的语言模型解析文献来收集关于相互作用类型和方向性的证据。此更新使用户能够分别可视化和访问三种不同的网络类型——功能网络、物理网络和调控网络，每种网络都适用于不同的研究需求。此外，通路富集检测功能也已更新，具有更好的错误发现率校正、冗余过滤和改进的可视化显示。该资源现在还提供了对聚类网络的改进注释，并为用户提供可下载的网络嵌入，这便于在机器学习中使用STRING网络，并允许蛋白质信息的跨物种转移。STRING数据库可在https://string-db.org/在线获取。
