Skip Navigation



Bioinformatics Advance Access published online on June 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti522
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/16/3360    most recent
bti522v1
Right arrow Alert me when this article is cited
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 Espadaler, J.
Right arrow Articles by Oliva, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Espadaler, J.
Right arrow Articles by Oliva, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 16, 2005
Accepted June 13, 2005

Article

Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships

Jordi Espadaler 1, Oriol Romero-Isart 2, Richard M. Jackson 2*, and Baldo Oliva 1

1 Grup de Bioinformàtica Estructural (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
2 School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, United Kingdom

* To whom correspondence should be addressed.
Richard M. Jackson, E-mail: jackson{at}bmb.leeds.ac.uk


  Abstract

Motivation: Given that association and dissociation of protein molecules is crucial in most biological processes, recently, several in silico methods have been developed to predict protein-protein interactions. Structural evidence has shown that usually interacting pairs of close homologues (interologues) physically interact in the same way. Moreover, conservation of an interaction depends on the conservation of the interface between interacting partners. In this paper we make use of both structural similarities between domains of known interacting proteins found in the Database of Interacting Proteins (DIP) and conservation of pairs of sequence patches involved in protein-protein interfaces to predict putative protein interaction pairs.

Results: We have obtained a large amount of putative protein-protein interaction (~130,000). The list is independent from other techniques both experimental and theoretical. We have split the list of predictions into three sets according to their relationship with known interacting proteins found in DIP. For each set, only a small fraction of the predicted protein pairs could be independently validated by cross checking with the Human Protein Reference Database (HPRD). The fraction of validated protein pairs was always larger than that expected by using random protein pairs. Furthermore, a correlation map of interacting protein pairs was calculated with respect to molecular function as defined in the Gene Ontology (GO) database. It shows good consistency of the predicted interactions with data in the HPRD database. The intersection between the lists of interactions of other methods and ours produces a network of potentially high-confidence interactions.


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
D. Aguilar, L. Skrabanek, S. S. Gross, B. Oliva, and F. Campagne
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
Nucleic Acids Res., June 1, 2008; 36(11): 3728 - 3737.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Guo, L. Yu, Z. Wen, and M. Li
Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
Nucleic Acids Res., May 1, 2008; 36(9): 3025 - 3030.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y.-C. Liao, M.-S. Lee, C.-Y. Ko, and C. A. Hsiung
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus
Bioinformatics, February 15, 2008; 24(4): 505 - 512.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Al-Shahrour, P. Minguez, J. Tarraga, I. Medina, E. Alloza, D. Montaner, and J. Dopazo
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W91 - W96.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. Dawelbait, C. Winter, Y. Zhang, C. Pilarsky, R. Grutzmann, J.-C. Heinrich, and M. Schroeder
Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data
Bioinformatics, July 1, 2007; 23(13): i115 - i124.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. J. Cockell, B. Oliva, and R. M. Jackson
Structure-based evaluation of in silico predictions of protein protein interactions using Comparative Docking
Bioinformatics, March 1, 2007; 23(5): 573 - 581.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
N. J. Burgoyne and R. M. Jackson
Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces
Bioinformatics, June 1, 2006; 22(11): 1335 - 1342.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Aragues, D. Jaeggi, and B. Oliva
PIANA: protein interactions and network analysis
Bioinformatics, April 15, 2006; 22(8): 1015 - 1017.
[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.