A clear systematic delineation of the interactions between phosphorylation sites on substrates and their effector kinases plays a fundamental role in revealing cellular activities, understanding signaling modulation mechanisms and proposing novel hypotheses. The emergence of bioinformatics tools contributes to studying phosphorylation network. Some of them feature the visualization of network, enabling more effective trace of the underlying biological problems in a clear and succinct way. In this review, we aimed to provide a toolbox for exploring phosphorylation network. We first systematically surveyed 19 tools that are available for exploring phosphorylation networks, and subsequently comparatively analyzed and summarized these tools to guide tool selection in terms of functionality, data sources, performance, network visualization and implementation, and finally briefly discussed the application cases of these tools. In different scenarios, the conclusion on the suitability of a tool for a specific user may vary. Nevertheless, easily accessible bioinformatics tools are proved to facilitate biological findings. Hopefully, this work might also assist non-specialists, students, as well as computational scientists who aim at developing novel tools in the field of phosphorylation modification.

中文翻译：

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用于探索蛋白质磷酸化网络的生物信息学工具箱。

对底物磷酸化位点与其效应激酶之间相互作用的清晰系统描绘在揭示细胞活动、理解信号调节机制和提出新假设方面发挥着重要作用。生物信息学工具的出现有助于研究磷酸化网络。其中一些具有网络可视化功能，能够以清晰简洁的方式更有效地追踪潜在的生物学问题。在这篇综述中，我们旨在提供一个工具箱来探索磷酸化网络。我们首先系统地调查了 19 种可用于探索磷酸化网络的工具，随后对这些工具进行了比较分析和总结，从功能、数据来源、性能、网络可视化和实现，最后简要讨论了这些工具的应用案例。在不同的场景中，对于特定用户的工具适用性的结论可能会有所不同。尽管如此，易于获取的生物信息学工具已被证明有助于生物学发现。希望这项工作也可以帮助非专家、学生以及旨在开发磷酸化修饰领域新工具的计算科学家。