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Comparative analysis and unification of domain-domain interaction networks
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2009 (English)In: Bioinformatics (Oxford, England), ISSN 1367-4811, Vol. 25, no 22, 3020-5 p.Article in journal (Refereed) Published
Abstract [en]

MOTIVATION: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain-domain interactions, and over nine datasets are available. Our aim is to analyse the coverage and quality of the existing resources, as well as the extent of their overlap. With this knowledge, we have the opportunity to merge individual domain interaction networks to construct a comprehensive and reliable database. RESULTS: In this article we introduce a new approach towards comparing domain-domain interaction networks. This approach is used to compare nine predicted domain and protein interaction networks. The networks were used to generate a database of unified domain interactions, UniDomInt. Each interaction in the dataset is scored according to the benchmarked reliability of the sources. The performance of UniDomInt is an improvement compared to the underlying source networks and to another composite resource, Domine. AVAILABILITY: http://sonnhammer.sbc.su.se/download/UniDomInt/

Place, publisher, year, edition, pages
2009. Vol. 25, no 22, 3020-5 p.
Keyword [en]
domain-domain interactions, unified domain interactions
National Category
Natural Sciences
Research subject
Biophysics; Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-35315DOI: 10.1093/bioinformatics/btp522ISI: 000271564300018PubMedID: 19720675OAI: oai:DiVA.org:su-35315DiVA: diva2:286948
Available from: 2010-01-15 Created: 2010-01-15 Last updated: 2014-03-17Bibliographically approved
In thesis
1. Protein Interactions from the Molecular to the Domain Level
Open this publication in new window or tab >>Protein Interactions from the Molecular to the Domain Level
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes.

Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes.

The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level.

In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2014. 52 p.
Keyword
Protein interactions, protein domains, membrane proteins
National Category
Bioinformatics (Computational Biology)
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-101795 (URN)978-91-7447-854-9 (ISBN)
Public defence
2014-04-25, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

Available from: 2014-04-03 Created: 2014-03-17 Last updated: 2014-07-07Bibliographically approved

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