Przulj Natasa, Kuchaiev Oleksii, Stevanović Aleksandar, Hayes Wayne
Department of Computer Science, University of California, Irvine, CA 92697-3425, USA.
Pac Symp Biocomput. 2010:178-89. doi: 10.1142/9789814295291_0020.
Understanding the evolution and structure of protein-protein interaction (PPI) networks is a central problem of systems biology. Since most processes in the cell are carried out by groups of proteins acting together, a theoretical model of how PPI networks develop based on duplications and mutations is an essential ingredient for understanding the complex wiring of the cell. Many different network models have been proposed, from those that follow power-law degree distributions and those that model complementarity of protein binding domains, to those that have geometric properties. Here, we introduce a new model for PPI network (and thus gene) evolution that produces well-fitting network models for currently available PPI networks. The model integrates geometric network properties with evolutionary dynamics of PPI network evolution.
理解蛋白质-蛋白质相互作用（PPI）网络的进化和结构是系统生物学的核心问题。由于细胞中的大多数过程是由协同作用的蛋白质组执行的，基于复制和突变的PPI网络如何发展的理论模型是理解细胞复杂连接的重要组成部分。已经提出了许多不同的网络模型，从遵循幂律度分布的模型、模拟蛋白质结合域互补性的模型，到具有几何特性的模型。在这里，我们引入了一种新的PPI网络（以及基因）进化模型，该模型为当前可用的PPI网络生成拟合良好的网络模型。该模型将几何网络特性与PPI网络进化的进化动力学相结合。
