结构域间相互作用在信号通路研究中的应用。

Applications of domain-domain interactions in pathway study.

作者信息

Ng Ka-Lok, Huang Chien-Hung, Liu Hsueh-Chuan, Liu Hsiang-Chuan

机构信息

Department of Bioinformatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung 413, Taiwan.

出版信息

Comput Biol Chem. 2008 Apr;32(2):81-7. doi: 10.1016/j.compbiolchem.2007.10.002. Epub 2007 Oct 22.

DOI:10.1016/j.compbiolchem.2007.10.002

PMID:18082454

Abstract

The domain combination pair approach is employed to derive putative protein domain-domain interactions (DDI) from the protein-protein interactions (PPI) database DIP. The results of putative DDI are computed for seven species. To determine the prediction performance, putative DDI results are compared with that of the database InterDom, where an average matching ratio of about 76% can be achieved. Several real PPI pathways are reconstructed based on the predicted DDI results. It is found that the pathways could be reconstructed with reasonable accuracy. Furthermore, a novel quantity, so called AP-order index, is introduced to predict the regulatory order for six PPI pathways. It is found that the AP-order index is a very reliable parameter to determine the regulatory order of PPI.

摘要

采用结构域组合对方法从蛋白质-蛋白质相互作用（PPI）数据库DIP中推导假定的蛋白质结构域-结构域相互作用（DDI）。计算了七个物种的假定DDI结果。为了确定预测性能，将假定的DDI结果与InterDom数据库的结果进行比较，可实现约76%的平均匹配率。基于预测的DDI结果重建了几条真实的PPI途径。发现这些途径可以以合理的准确性重建。此外，引入了一个新的量，即所谓的AP序指数，来预测六条PPI途径的调控顺序。发现AP序指数是确定PPI调控顺序的非常可靠的参数。