New Public-Access Source With 3-D Information for Protein Interactions

Researchers have developed a platform that compiles all the atomic data, previously stored in diverse databases, on protein structures and protein interactions for eight organisms of relevance. They apply a singular homology-based modelling procedure.

The scientists Roberto Mosca, Arnaud Ceol and Patrick Aloy provide the international biomedical community withInteractome3D (, an open-access and free web platform developed entirely by the Institute for Research in Biomedicine (IRB Barcelona).Interactome 3D offers for the first time the possibility to anonymously access and add molecular details of protein interactions and to obtain the information in 3D models. For researchers, atomic level details about the reactions are fundamental to unravel the bases of biology, disease development, and the design of experiments and drugs to combat diseases.
Interactome 3D provides reliable information about more than 12,000 protein interactions for eight model organisms, namely the plant Arabidopsis thaliana, the worm Caenorhabditis elegans, the fly Drosophila melanogaster, the bacteria Escherichia coli andHelicobacter pylori, the brewer’s yeast Saccharomyces cerevisiae, the mouse Mus musculus, and Homo sapiens. These models are considered the most relevant in biomedical research and genetic studies. The journalNature Methods presents the research results and accredits the platform on the basis of it high reliability and precision in modelling interactions, which reaches an average of 75%.
Further details can be found at:
Interactome3D: adding structural details to protein networks by Roberto Mosca, Arnaud Céol and Patrick Aloy. (Nature Methods(2012) doi:10.1038/nmeth.2289)
Network-centered approaches are increasingly used to understand the fundamentals of biology. However, the molecular details contained in the interaction networks, often necessary to understand cellular processes, are very limited, and the experimental difficulties surrounding the determination of protein complex structures make computational modeling techniques paramount. Here we present Interactome3D, a resource for the structural annotation and modeling of protein-protein interactions. Through the integration of interaction data from the main pathway repositories, we provide structural details at atomic resolution for over 12,000 protein-protein interactions in eight model organisms. Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner. Finally, we illustrate the value of Interactome3D through the structural annotation of the complement cascade pathway, rationalizing a potential common mechanism of action suggested for several disease-causing mutations.
Interesting not only for its implications for bioinformatics but for the development of homology modeling (superficially, similar proteins have similar interaction sites) to assist in their work.
The topic map analogy would be to show a subject domain, different identifications of the same subject tend to have the same associations or to fall into other patterns.
Then constructing a subject identity test based upon a template of associations or other values.