Das Barnali, Mitra Pralay
Department of Computer Science and Engineering, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India.
J Mol Model. 2022 May 25;28(6):167. doi: 10.1007/s00894-022-05133-8.
The modular organization of a cell which can be determined by its interaction network allows us to understand a mesh of cooperation among the functional modules. Therefore, cellular-level identification of functional modules aids in understanding the functional and structural characteristics of the biological network of a cell and also assists in determining or comprehending the evolutionary signal. We develop ProMoCell that performs real-time Web scraping for generating clusters of the cellular level functional units of an organism. ProMoCell constructs the Protein Locality Graphs and clusters the cellular level functional units of an organism by utilizing experimentally verified data from various online sources. Also, we develop ProModb, a database service that houses precomputed whole-cell protein-protein interaction network-based functional modules of an organism using ProMoCell. Our Web service is entirely synchronized with the KEGG pathway database and allows users to generate spatially localized protein modules for any organism belonging to the KEGG genome using its real-time Web scraping characteristics. Hence, the server will host as many organisms as is maintained by the KEGG database. Our Web services provide the users a comprehensive and integrated tool for an efficient browsing and extraction of the spatial locality-based protein locality graph and the functional modules constructed by gathering experimental data from several interaction databases and pathway maps. We believe that our Web services will be beneficial in pharmacological research, where a novel research domain called modular pharmacology has initiated the study on the diagnosis, prevention, and treatment of deadly diseases using functional modules.
细胞的模块化组织可由其相互作用网络确定，这使我们能够理解功能模块之间的合作网络。因此，细胞水平上功能模块的识别有助于理解细胞生物网络的功能和结构特征，也有助于确定或理解进化信号。我们开发了ProMoCell，它通过实时网络抓取来生成生物体细胞水平功能单元的聚类。ProMoCell构建蛋白质局部性图，并利用来自各种在线来源的实验验证数据对生物体的细胞水平功能单元进行聚类。此外，我们还开发了ProModb，这是一种数据库服务，它使用ProMoCell存储基于全细胞蛋白质-蛋白质相互作用网络的生物体预计算功能模块。我们的网络服务与KEGG通路数据库完全同步，允许用户利用其实时网络抓取特性为任何属于KEGG基因组的生物体生成空间定位的蛋白质模块。因此，该服务器将托管与KEGG数据库所维护数量相同的生物体。我们的网络服务为用户提供了一个全面且集成的工具，用于高效浏览和提取基于空间局部性的蛋白质局部性图以及通过收集来自多个相互作用数据库和通路图的实验数据构建的功能模块。我们相信，我们的网络服务将在药理学研究中发挥作用，在该研究领域，一个名为模块化药理学的新研究方向已开始利用功能模块对致命疾病的诊断、预防和治疗进行研究。
