Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College, London, UK.
Bioinformatics. 2012 May 1;28(9):1239-45. doi: 10.1093/bioinformatics/bts119. Epub 2012 Mar 13.
Analysis of protein-protein interaction networks (PPINs) at the system level has become increasingly important in understanding biological processes. Comparison of the interactomes of different species not only provides a better understanding of species evolution but also helps with detecting conserved functional components and in function prediction. Method and
Here we report a PPIN alignment method, called PINALOG, which combines information from protein sequence, function and network topology. Alignment of human and yeast PPINs reveals several conserved subnetworks between them that participate in similar biological processes, notably the proteasome and transcription related processes. PINALOG has been tested for its power in protein complex prediction as well as function prediction. Comparison with PSI-BLAST in predicting protein function in the twilight zone also shows that PINALOG is valuable in predicting protein function.
The PINALOG web-server is freely available from http://www.sbg.bio.ic.ac.uk/~pinalog. The PINALOG program and associated data are available from the Download section of the web-server.
Supplementary data are available at Bioinformatics online.
在系统水平上分析蛋白质-蛋白质相互作用网络（PPINs）在理解生物过程方面变得越来越重要。比较不同物种的相互作用组不仅可以更好地了解物种进化，还有助于检测保守的功能组件和功能预测。方法和结果：在这里，我们报告了一种称为 PINALOG 的 PPIN 对齐方法，该方法结合了蛋白质序列、功能和网络拓扑结构的信息。对人类和酵母 PPINs 的对齐揭示了它们之间存在几个参与相似生物过程的保守子网，特别是蛋白酶体和转录相关过程。PINALOG 已在蛋白质复合物预测和功能预测方面进行了测试。与 PSI-BLAST 在预测“黄昏区”蛋白质功能的比较也表明，PINALOG 在预测蛋白质功能方面很有价值。可用性和实现：PINALOG 网络服务器可从 http://www.sbg.bio.ic.ac.uk/~pinalog 免费获得。PINALOG 程序和相关数据可从网络服务器的“下载”部分获得。联系人：m.sternberg@imperial.ac.uk补充信息：补充数据可在 Bioinformatics 在线获得。
