Büchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dräger, Andreas and Schröder, Adrian and Zell, Andreas

ProDGe: investigating protein-protein interactions at the domain level

, Nature Precedings (2011)


Abstract

An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java™ program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species. We further evaluated and compared experimentally identified protein interactions from IntAct with domain interactions from DOMINE for six species and noticed that 31.13% of all IntAct protein interactions in all six species can be mapped to the actual interacting domains. ProDGe and a comprehensive documentation are freely available at http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe.


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BibTeX

@techreport{Buechel2011a,
  author = {B\"uchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dr\"ager,
	Andreas and Schr\"oder, Adrian and Zell, Andreas},
  title = {{ProDGe: investigating protein-protein interactions at the domain
	level}},
  institution = {Nature Precedings},
  year = {2011},
  month = aug,
  abstract = {An important goal of systems biology is the identification and investigation
	of known and predicted protein-protein interactions to obtain more
	information about new cellular pathways and processes. Proteins interact
	via domains, thus it is important to know which domains a protein
	contains and which domains interact with each other. Here we present
	the Java\texttrademark{} program ProDGe (Protein Domain Gene), which
	visualizes existing and suggests novel domain-domain interactions
	and protein-protein interactions at the domain level. The comprehensive
	dataset behind ProDGe consists of protein, domain and interaction
	information for both layers, collected and combined appropriately
	from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions,
	ProDGe suggests novel protein interactions and assigns them to four
	confidence classes, depending on the reliability of the underlying
	domain interaction. Furthermore, ProDGe is able to identify potential
	homologous interaction partners in other species, which is particularly
	helpful when investigating poorly annotated species. We further evaluated
	and compared experimentally identified protein interactions from
	IntAct with domain interactions from DOMINE for six species and noticed
	that 31.13% of all IntAct protein interactions in all six species
	can be mapped to the actual interacting domains. ProDGe and a comprehensive
	documentation are freely available at \url{http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe}.},
  doi = {10.1038/npre.2011.6188.1},
  keywords = {protein, domain, interaction, domain-domain interaction, interaction
	visualization, protein-protein interaction},
  pdf = {http://precedings.nature.com/documents/6188/version/1/files/npre20116188-1.pdf},
  url = {http://precedings.nature.com/documents/6188/version/1}
}