Predicting and analyzing protein interaction networks

大规模的蛋白质相互作用网络已经通过实验确定了几个 生物，这些网络的计算分析提供了新的机会，以揭示 蛋白质的功能和途径。与此同时，尽管情况有所改善， 虽然高通量技术，但在不久的将来将它们应用于所有测序的 基因组因此，对于绝大多数测序的基因组，只有一小部分已知蛋白质 已经通过实验确定了相互作用，并且新颖 计算方法提供了一个有前途的，替代的手段，建立大，高， 置信交互图。这项研究的广泛，长期目标是建立一个 通过开发算法来理解蛋白质相互作用的综合研究计划 用于分析和预测蛋白质相互作用图谱的互补问题。我们的具体 目标是：（1）开发利用全基因组蛋白质相互作用拓扑结构的算法 图和蛋白质功能之间的关系，以作出新的预测， 蛋白质的生物过程。(2)建立一个系统来询问蛋白质相互作用网络 使用“模板”指定共同的互动模式或途径，以帮助发现 新奇的例子。(3)开发通用结构生物信息学方法， 特定蛋白质相互作用界面的性质，并应用这种方法，以帮助 在基因组水平预测Cys 2 HiS 2锌指蛋白-DNA相互作用。总之，我们 我希望所提出的工具将显着推进最先进的计算 在蛋白质的细胞相互作用、途径和 网络.所有软件和预测将通过互联网公开提供。

Large-scale protein interaction networks have been determined experimentally for several organisms, and computational analysis of these networks provides new opportunities to uncover protein functions and pathways. At the same time, despite improvements in high-throughput technologies, it is still not feasible in the near future to apply them to all sequenced genomes. Thus, for the vast majority of sequenced genomes, only a small fraction of known protein interactions have been experimentally determined, and novel computational approaches provide a promising, alternative means for building large, high- confidence interaction maps. The broad, long-term goal of this research is to build a comprehensive research program for understanding protein interactions, by developing algorithms for the complementary problems of analyzing and predicting protein interaction maps. Our specific aims are: (1) To develop algorithms that exploit the topology of whole-genome protein interaction maps and the relationships between protein functions, in order to make novel predictions about a protein's biological process. (2) To build a system for interrogating protein interaction networks using "templates" specifying common patterns of interactions or pathways, in order to help uncover novel instances. (3) To develop a general structural bioinformatics approach for leveraging properties of specific protein interaction interfaces, and to apply this approach in order to help predict Cys2HiS2 zinc finger protein-DNA interactions at the genomic scale. Taken together, we hope that the proposed tools will significantly advance the state-of-the-art in computational approaches for characterizing proteins within the context of their cellular interactions, pathways and networks. All software and predictions will be made publicly available via the internet.