Skip Navigation



Bioinformatics Advance Access published online on November 14, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl566
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/2/245    most recent
btl566v1
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 Kim, S.
Right arrow Articles by Vannucci, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kim, S.
Right arrow Articles by Vannucci, M.
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 August 22, 2006
Revised November 6, 2006
Accepted November 7, 2006

Applications note

Detecting protein dissimilarities in multiple alignments using Bayesian variable selection

Sinae Kim 1, Jerry Tsai 2, Ioannis Kagiampakis 2, Patricia LiWang 2, and Marina Vannucci 3 *

1 Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
2 Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
3 Department of Statistics, Texas A&M University, College Station, TX, USA

* To whom correspondence should be addressed.
Marina Vannucci, E-mail: mvannucci{at}stat.tamu.edu


  Abstract

Motivation: We present an application of Bayesian variable selection to the novel detection of sequence elements that confer negative design to protein structure and function. As an illustration, we analyze the different dimer interfaces between the CXCL8 chemokine family with the CCL4 and CCL2 chemokine families to discover the changes that disfavor CXCL8 of quaternary structure.

Results: In comparison with known experimental results, our method identifies evolutionarily conserved sequence changes in the CC families that inhibit CXCL8 quaternary structure. Therefore, we find positive selection of negative design elements. Furthermore, our approach predicts that a two-residue deletion conserved in the CCL4 chemokine family disfavors CXCL8 dimerization.

Availability: The Matlab code for the Bayesian variable selection should be distributed for non-commercial purposes only and is freely available at http://stat.tamu.edu/~mvannucci/webpages/codes.html.

Associate Editor: Martin Bishop
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
 Proc. Natl. Acad. Sci. USAHome page
E. Akiva, Z. Itzhaki, and H. Margalit
Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains
PNAS, September 9, 2008; 105(36): 13292 - 13297.
[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.