Skip Navigation

Bioinformatics 2008 24(16):i35-i41; doi:10.1093/bioinformatics/btn290
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Schelhorn, S.-E.
Right arrow Articles by Albrecht, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schelhorn, S.-E.
Right arrow Articles by Albrecht, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

An integrative approach for predicting interactions of protein regions

Sven-Eric Schelhorn , Thomas Lengauer and Mario Albrecht *

Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: Protein–protein interactions are commonly mediated by the physical contact of distinct protein regions. Computational identification of interacting protein regions aids in the detailed understanding of protein networks and supports the prediction of novel protein interactions and the reconstruction of protein complexes.

Results: We introduce an integrative approach for predicting protein region interactions using a probabilistic model fitted to an observed protein network. In particular, we consider globular domains, short linear motifs and coiled-coil regions as potential protein-binding regions. Possible cooperations between multiple regions within the same protein are taken into account. A finegrained confidence system allows for varying the impact of specific protein interactions and region annotations on the modeling process. We apply our prediction approach to a large training set using a maximum likelihood method, compare different scoring functions for region interactions and validate the predicted interactions against a collection of experimentally observed interactions. In addition, we analyze prediction performance with respect to the inclusion of different region types, the incorporation of confidence values for training data and the utilization of predicted protein interactions.

Contact: mario.albrecht{at}mpi-inf.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, and H.-W. Mewes
CORUM: the comprehensive resource of mammalian protein complexes--2009
Nucleic Acids Res., November 1, 2009; (2009) gkp914v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Blankenburg, F. Ramirez, J. Buch, and M. Albrecht
DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W122 - W128.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Blankenburg, R. D. Finn, A. Prlic, A. M. Jenkinson, F. Ramirez, D. Emig, S.-E. Schelhorn, J. Buch, T. Lengauer, and M. Albrecht
DASMI: exchanging, annotating and assessing molecular interaction data
Bioinformatics, May 15, 2009; 25(10): 1321 - 1328.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.