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/.

中文翻译：

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2025 年的 STRING 数据库：具有调控方向性的蛋白质网络


蛋白质相互合作、调节和结合以实现其功能。了解它们相互作用的复杂网络对于细胞过程的系统级描述至关重要。STRING 数据库对从实验分析、计算预测和先验知识中提取的蛋白质-蛋白质关联信息进行编译、评分和整合。其目标是创建全面而客观的全球网络，包括物理和功能交互。此外，STRING 还提供补充工具，例如网络聚类和通路富集分析。最新版本 STRING 12.5 引入了一个新的“调节网络”，为此，它使用精选的通路数据库和解析文献的微调语言模型收集有关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、物理和监管），每种网络类型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、冗余过滤和改进的视觉显示。该资源现在还提供改进的聚类网络注释，并为用户提供可下载的网络嵌入，这有助于在机器学习中使用 STRING 网络，并允许蛋白质信息的跨物种传输。STRING 数据库可在 https://string-db.org/ 在线获取。