Decomposing protein networks into domain–domain interactions
Open Access
- 1 September 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 21 (suppl_2), ii220-ii221
- https://doi.org/10.1093/bioinformatics/bti1135
Abstract
Summary: 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. Availability: Both Cytoscape plugins can be downloaded from http://www.cytoscape.org Contact:mario.albrecht@mpi-inf.mpg.deKeywords
This publication has 8 references indexed in Scilit:
- The Universal Protein Resource (UniProt)Nucleic Acids Research, 2006
- Protein complexes: structure prediction challenges for the 21st centuryCurrent Opinion in Structural Biology, 2005
- The evolution of domain arrangements in proteins and interaction networksCellular and Molecular Life Sciences, 2005
- 3did: interacting protein domains of known three-dimensional structureNucleic Acids Research, 2004
- Protein interaction networks from yeast to humanCurrent Opinion in Structural Biology, 2004
- Ataxin-7 is a subunit of GCN5 histone acetyltransferase-containing complexesHuman Molecular Genetics, 2004
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003
- InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexesNucleic Acids Research, 2003