Abstract：
Proteome-wide characterization of protein-protein interactions (PPIs) is crucial to understand the functional roles of protein machinery within cells systematically. With the accumulation of PPI data in different plants, the interaction details of binary PPIs, such as the three-dimensional (3D) structural contexts of interaction sites/interfaces, are urgently demanded. To meet this requirement, we have developed a comprehensive and easy-to-use database called PlaPPISite ( http://zzdlab.com/plappisite/index.php ) to present interaction details for 13 plant interactomes. Here, we provide a clear guide on how to search and view protein interaction details through the PlaPPISite database. Firstly, the running environment of our database is introduced. Secondly, the input file format is briefly introduced. Moreover, we discussed which information related to interaction sites can be achieved through several examples. In addition, some notes about PlaPPISite are also provided. More importantly, we would like to emphasize the importance of interaction site information in plant systems biology through this user guide of PlaPPISite. In particular, the easily accessible 3D structures of PPIs in the coming post-AlphaFold2 era will definitely boost the application of plant interactome to decipher the molecular mechanisms of many fundamental biological issues.
摘要：
蛋白质-蛋白质相互作用（PPI）的全蛋白质组表征对于系统地了解细胞内蛋白质机制的功能作用至关重要。随着PPI数据在不同植物中的积累，二进制PPI的交互细节，例如交互站点/接口的三维(3D)结构上下文，迫切需要。为了满足这一要求，我们开发了一个全面且易于使用的数据库，称为PlaPPISite（http://zzdlab.com/plaappisite/index。php)提供13个植物相互作用的相互作用细节。这里,我们提供了有关如何通过PlaPPISite数据库搜索和查看蛋白质相互作用细节的清晰指南.首先,介绍了数据库的运行环境。其次,简单介绍了输入文件格式。此外，我们通过几个例子讨论了哪些与交互网站相关的信息可以实现。此外,还提供了一些关于PlaPPISite的注释。更重要的是,我们想通过PlaPPISite的用户指南强调植物系统生物学中相互作用位点信息的重要性。特别是,在即将到来的后AlphaFold2时代，PPI的3D结构容易获得，这肯定会促进植物相互作用组的应用，以破译许多基本生物学问题的分子机制。
