Skip Navigation


Bioinformatics Advance Access originally published online on October 31, 2007
Bioinformatics 2007 23(23):3139-3146; doi:10.1093/bioinformatics/btm503
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
23/23/3139    most recent
btm503v1
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 ISI Web of Science
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 Sommer, I.
Right arrow Articles by Lengauer, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sommer, I.
Right arrow Articles by Lengauer, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Moment invariants as shape recognition technique for comparing protein binding sites

Ingolf Sommer 1,*, Oliver Müller 1, Francisco S. Domingues 1, Oliver Sander 1, Joachim Weickert 2 and Thomas Lengauer 1

1Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken and 2Faculty of Mathematics and Computer Science, Saarland University, Building E1.1, 66041 Saarbrücken, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: An approach for identifying similarities of protein–protein binding sites is presented. The geometric shape of a binding site is described by computing a feature vector based on moment invariants. In order to search for similarities, feature vectors of binding sites are compared. Similar feature vectors indicate binding sites with similar shapes.

Results: The approach is validated on a representative set of protein–protein binding sites, extracted from the SCOPPI database. When querying binding sites from a representative set, we search for known similarities among 2819 binding sites. A median area under the ROC curve of 0.98 is observed. For half of the queries, a similar binding site is identified among the first two of 2819 when sorting all binding sites according the proposed similarity measure. Typical examples identified by this method are analyzed and discussed. The nitrogenase iron protein-like SCOP family is clustered hierarchically according to the proposed similarity measure as a case study.

Availability: Python code is available on request from the authors.

Contact: sommer{at}mpi-inf.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on July 7, 2007; revised on September 13, 2007; accepted on October 2, 2007

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.