Kim Woo-Yeon, Kang Sungsoo, Kim Byoung-Chul, Oh Jeehyun, Cho Seongwoong, Bhak Jong, Choi Jong-Soon
Korean BioInformation Center, KRIBB, Daejeon 305-806, Korea.
BMC Bioinformatics. 2008;9 Suppl 1(Suppl 1):S20. doi: 10.1186/1471-2105-9-S1-S20.
Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date.
We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category.
SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.
蓝藻是用于研究光合作用、碳氮同化、植物质体进化以及对环境胁迫适应性的模式生物。尽管对蓝藻进行了许多研究，但迄今为止尚无基于网络的其调控和信号蛋白-蛋白相互作用网络的数据库。
我们报告了一个名为SynechoNET的数据库和网站，它提供预测的蛋白-蛋白相互作用。SynechoNET展示了蓝藻结构域-结构域相互作用以及使用模式蓝藻集胞藻PCC 6803的蛋白水平相互作用。它利用包含相互补充和冗余数据的公共相互作用数据库来预测蛋白-蛋白相互作用。此外，SynechoNET提供有关跨膜拓扑结构、信号肽和结构域结构的信息，以支持对调控膜蛋白的分析。这些生物学信息可以在用户友好的网络界面中进行查询和可视化，这些界面包括交互式网络查看器以及按关键词和功能类别搜索的页面。
SynechoNET是一个集成的蛋白-蛋白相互作用数据库，旨在分析蓝藻中的调控膜蛋白。它为生物学家提供了一个平台，通过预测集胞藻蛋白的相互作用伙伴、膜关联和膜拓扑结构来扩展蓝藻的基因组数据。SynechoNET可在http://synechocystis.org/ 或直接在http://bioportal.kobic.kr/SynechoNET/免费获取。
