University of Malaga and CIBER de Enfermedades Raras, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Instituto de Salud Carlos III, Spain.
BMC Bioinformatics. 2009 Oct 15;10 Suppl 12(Suppl 12):S17. doi: 10.1186/1471-2105-10-S12-S17.
Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data http://asp.uma.es.
The tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein.
The tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks.
蛋白质-蛋白质相互作用可以被视为生物自我组织和动态平衡的基本骨架。目前已经获得了大量的实验数据，而计算工具对于整合和组织这些信息至关重要。本文介绍了 Protopia，这是一种生物学工具，它提供了一种在不同的蛋白质相互作用网络数据库中搜索蛋白质及其相互作用的方法，这是我们机构进行生物数据整合的多学科倡议的一部分，该倡议的网址是 http://asp.uma.es。
该工具可以访问不同的数据库（目前是免费版的 Transfac、DIP、Hprd、Int-Act 和 iHop），结果以生物蛋白质名称或数据库代码的形式表示，可以表示为向量或矩阵。它们可以作为有机图进行交互式表示和处理。通过为每个蛋白质注释的 Uniprot 代码，可以在数据库之间进行比较。
该工具定位并整合了上述数据库中当前存储的信息，并检测到了它们之间的冗余。结果与最重要的网络分析器兼容，因此可以与其他全球知名的工具和平台进行比较和分析。可视化的可能性有助于实现这一目标，对于处理多步骤或复杂网络来说尤其有趣。
