Decomposing protein networks into domain-domain interactions.
The application of novel experimental techniques has generated large networks of protein-protein interactions. Frequently, important information on the structure and cellular function of protein-protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and computes a putative network of corresponding domain-domain interactions. To this end, the network graph of proteins has been extended by additional node and edge types for domain interactions, including different node and edge shapes and coloring schemes used for visualization. An additional plugin provides supplementary web links to Internet resources on domain function and structure.


BACKGROUND
Both Cytoscape plugins can be downloaded from http://www.cytoscape.org
Albrecht
Mario
M
Max Planck Institute for Informatics, Saarbrücken, Germany. mario.albrecht@mpi-inf.mpg.de
Huthmacher
Carola
C
Tosatto
Silvio C E
SC
Lengauer
Thomas
T
D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D011506:Proteins