On the detection of functionally coherent groups of protein domains with an extension to protein annotation

Background: Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinations are limited in their scope, e.g. to the identification of combinations falling within individual proteins or within specific regions in a translated genome. Further effort is needed to identify groups of domains that span across two or more proteins and are linked by a cooperative function. Such functional domain combinations can be useful for protein annotation. Results: Using a new computational method, we have identified 114 groups of domains, referred to as domain assembly units (DASSEM units), in the proteome of budding yeast Saccharomyces cerevisiae. The units participate in many important cellular processes such as transcription regulation, translation initiation, and mRNA splicing. Within the units the domains were found to function in a cooperative manner...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: William A. McLaughlin, Ken Chen, Tingjun Hou, Wei Wang
• Keywords: BMCBI 2007, Domain Combinations, Functional Domain Combinations, Protein