State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.
BMC Plant Biol. 2020 Feb 6;20(1):61. doi: 10.1186/s12870-020-2254-4.
Protein-protein interactions (PPIs) play very important roles in diverse biological processes. Experimentally validated or predicted PPI data have become increasingly available in diverse plant species. To further explore the biological functions of PPIs, understanding the interaction details of plant PPIs (e.g., the 3D structural contexts of interaction sites) is necessary. By integrating bioinformatics algorithms, interaction details can be annotated at different levels and then compiled into user-friendly databases. In our previous study, we developed AraPPISite, which aimed to provide interaction site information for PPIs in the model plant Arabidopsis thaliana. Considering that the application of AraPPISite is limited to one species, it is very natural that AraPPISite should be evolved into a new database that can provide interaction details of PPIs in multiple plants.
PlaPPISite (http://zzdlab.com/plappisite/index.php) is a comprehensive, high-coverage and interaction details-oriented database for 13 plant interactomes. In addition to collecting 121 experimentally verified structures of protein complexes, the complex structures of experimental/predicted PPIs in the 13 plants were also constructed, and the corresponding interaction sites were annotated. For the PPIs whose 3D structures could not be modelled, the associated domain-domain interactions (DDIs) and domain-motif interactions (DMIs) were inferred. To facilitate the reliability assessment of predicted PPIs, the source species of interolog templates, GO annotations, subcellular localizations and gene expression similarities are also provided. JavaScript packages were employed to visualize structures of protein complexes, protein interaction sites and protein interaction networks. We also developed an online tool for homology modelling and protein interaction site annotation of protein complexes. All data contained in PlaPPISite are also freely available on the Download page.
PlaPPISite provides the plant research community with an easy-to-use and comprehensive data resource for the search and analysis of protein interaction details from the 13 important plant species.
蛋白质-蛋白质相互作用（PPIs）在各种生物过程中起着非常重要的作用。在不同的植物物种中，实验验证或预测的 PPI 数据变得越来越丰富。为了进一步探索 PPIs 的生物学功能，了解植物 PPIs 的相互作用细节（例如，相互作用位点的 3D 结构环境）是必要的。通过整合生物信息学算法，可以在不同的水平上注释相互作用细节，然后将其编译成用户友好的数据库。在我们之前的研究中，我们开发了 AraPPISite，旨在为拟南芥模型植物中的 PPIs 提供相互作用位点信息。考虑到 AraPPISite 的应用仅限于一个物种，因此很自然地应该将 AraPPISite 演变成一个新的数据库，该数据库可以提供多种植物中 PPIs 的相互作用细节。
PlaPPISite（http://zzdlab.com/plappisite/index.php）是一个综合性的、高覆盖率的、面向相互作用细节的数据库，用于 13 种植物的相互作用组。除了收集 121 个实验验证的蛋白质复合物结构外，还构建了这 13 种植物中实验/预测的 PPI 的复合物结构，并对相应的相互作用位点进行了注释。对于无法建模的 PPI，推断了相关的结构域-结构域相互作用（DDIs）和结构域-基序相互作用（DMIs）。为了便于评估预测 PPI 的可靠性，还提供了同源模板的来源物种、GO 注释、亚细胞定位和基因表达相似性。使用 JavaScript 包可视化蛋白质复合物、蛋白质相互作用位点和蛋白质相互作用网络的结构。我们还开发了一个用于同源建模和蛋白质复合物相互作用位点注释的在线工具。PlaPPISite 中包含的所有数据也可在下载页面上免费获取。
PlaPPISite 为植物研究界提供了一个易于使用的综合数据资源，用于搜索和分析来自 13 种重要植物物种的蛋白质相互作用细节。
