Skip Navigation



Bioinformatics Advance Access published online on July 26, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl382
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
22/18/2237    most recent
btl382v1
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 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 (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 30, 2006
Revised July 4, 2006
Accepted July 6, 2006

Article

Identification of function-associated loop motifs and application to protein function prediction

Jordi Espadaler 1, Enrique Querol 2, Francesc X. Aviles 2, and Baldo Oliva 3 *

1 Grup de Bioinformàtica Estructural (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003-Barcelona, Catalonia, Spain; Institut de Biotecnologia i Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193-Bellaterra (Barcelona), Catalonia, Spain
2 Institut de Biotecnologia i Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193-Bellaterra (Barcelona), Catalonia, Spain
3 Grup de Bioinformàtica Estructural (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003-Barcelona, Catalonia, Spain

* To whom correspondence should be addressed.
Baldo Oliva, E-mail: boliva{at}imim.es


  Abstract

Motivation: The detection of function-related local 3D-motifs in protein structures can provide insights towards protein function in absence of sequence or fold similarity. Protein loops are known to play important roles in protein function and several loop classifications have been described, but the automated identification of putative functional 3D-motifs in such classifications has not yet been addressed. This identification can be used on sequence annotations.

Results: We evaluated three different scoring methods for their ability to identify known motifs from the PROSITE database in ArchDB. More than 500 new putative function-related motifs not reported in PROSITE were identified. Sequence patterns derived from these motifs were especially useful at predicting precise annotations. The number of reliable sequence annotations could be increased up to 100% with respect to standard BLAST.

Associate Editor: Anna Tramontano
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




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.