Skip Navigation



Bioinformatics Advance Access published online on January 18, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl654
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/5/555    most recent
btl654v2
btl654v1
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 Bernauer, J.
Right arrow Articles by Poupon, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bernauer, J.
Right arrow Articles by Poupon, A.
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

A new protein-protein docking scoring function based on interface residue properties

J. Bernauer 1, J. Azé 2, J. Janin 1 and A. Poupon 1,*

1Yeast Structural Genomics – IBBMC UMR 8619 – Bâtiment 430 – Université Paris-Sud – 91405 ORSAY –- FRANCE
2Equipe de Bioinformatique – LRI UMR 8623– Bâtiment 430 – Université Paris-Sud – 91405 ORSAY –- FRANCE

*To whom correspondence should be addressed. Anne Poupon, E-mail: anne{at}rezo.net


  Abstract

Motivation: Protein-protein complexes are known to play key roles in many cellular processes. However, they are often not accessible to experimental study because of their low stability and difficulty to produce the proteins and assemble them in native conformation. Thus, docking algorithms have been developed to provide an in silico approach of the problem. A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate solutions, and then a scoring function is used to rank them.

Results: To address the second step, we developed a scoring function based on a Voronoï tessellation of the protein three-dimensional structure. We showed that the Voronoï representation may be used to describe in a simplified but useful manner, the geometric and physico-chemical complementarities of two molecular surfaces. We measured a set of parameters on native protein-protein complexes and on decoys, and used them as attributes in several statistical learning procedures: a logistic function, Support Vector Machines (SVM), and a genetic algorithm. For the later, we used ROGER, a genetic algorithm designed to optimize the area under the ROC curve. To further test the scores derived with ROGER, we ranked models generated by two different docking algorithms on targets of a blind prediction experiment, improving in almost all cases the rank of native-like solutions.

Availability: http://genomics.eu.org/spip/-Bioinformatics-tools-

Associate Editor: Anna Tramontano

Received on September 15, 2006; revised on December 21, 2006; accepted on December 21, 2006

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
 BioinformaticsHome page
J. Bernauer, R. P. Bahadur, F. Rodier, J. Janin, and A. Poupon
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions
Bioinformatics, March 1, 2008; 24(5): 652 - 658.
[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.