InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes

Abstract

Advances in proteomics technology have enabled new proteins to be discovered at an unprecedented speed, and high throughput experimental methods have been developed to detect protein interactions and complexes en masse. Such bottom-up, data-driven approach has resulted in data that may be uninformative or potentially errorful, requiring further validation and annotation. The InterDom database focuses on providing supporting evidence for the detected protein interactions based on putative protein domain interactions. Using an integrative approach, InterDom derives potential domain interactions by combining data from multiple sources, ranging from domain fusions, protein interactions and complexes, to scientific literature. The InterDom database is available at http://InterDom.lit.org.sg.

Figure 1

Comparison of connected graph structures for six septin-complex members (shown colored gray) based on high-throughput experimental detection methods and putative domain–domain interactions from InterDom. (A) The graph structure on the top shows the relationships between the six septin-complex members associated by high throughput detection methods as reported in Box 2 of von Mering et al., reproduced here for comparison by permission from Nature (4) copyright (2002) Macmillan Publishers Ltd. The dotted and solid boxes show the complex components detected using TAP purification and HMS-PCI purification methods respectively, and the gray links show the interacting protein components based on two-hybrid interaction. None of the three experimental methods singularly identifies the six members of the septin complex. (B) The graph structure at the bottom shows the result of using InterDoms domain–domain interactions to link up the six septin components and the three non-septin proteins. A link is established between two proteins if there is at least one putative domain–domain interaction between them. In this case, all the six septin-complex proteins were found to be fully connected with putative domain–domain interaction links.

Figure 1

Comparison of connected graph structures for six septin-complex members (shown colored gray) based on high-throughput experimental detection methods and putative domain–domain interactions from InterDom. (A) The graph structure on the top shows the relationships between the six septin-complex members associated by high throughput detection methods as reported in Box 2 of von Mering et al., reproduced here for comparison by permission from Nature (4) copyright (2002) Macmillan Publishers Ltd. The dotted and solid boxes show the complex components detected using TAP purification and HMS-PCI purification methods respectively, and the gray links show the interacting protein components based on two-hybrid interaction. None of the three experimental methods singularly identifies the six members of the septin complex. (B) The graph structure at the bottom shows the result of using InterDoms domain–domain interactions to link up the six septin components and the three non-septin proteins. A link is established between two proteins if there is at least one putative domain–domain interaction between them. In this case, all the six septin-complex proteins were found to be fully connected with putative domain–domain interaction links.