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Bioinformatics Advance Access published online on November 14, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti773
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 2, 2005
Revised October 19, 2005
Accepted November 8, 2005

Discovery note

"Protein Peeling": an approach for splitting a 3D protein structure into compact fragments

Jean-Christophe Gelly 1, Alexandre G. de Brevern 2 *, and Serge Hazout 2 {dagger}

1 INSERM, U726, Equipe de Bioinformatique Génomique & Moléculaire (EBGM), Paris, F-75005 France; Université Denis Diderot - Paris 7, case 7113, 75251 Paris Cedex 05, France; CNRS, UMR 7602, Institut de Minéralogie et Physique des Milieux Condensés (IMPMC), Paris, F-75005 France; Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris Cedex 05, France
2 INSERM, U726, Equipe de Bioinformatique Génomique & Moléculaire (EBGM), Paris, F-75005 France; Université Denis Diderot - Paris 7, case 7113, 75251 Paris Cedex 05, France

* To whom correspondence should be addressed.
Alexandre G. de Brevern, E-mail: debrevern{at}ebgm.jussieu.fr


  Abstract

Motivation: The object of this study is to propose a new method to identify small compact units that compose the protein three dimensional structures. These fragments, called "protein units (PU)", are a new level of description to well understand and analyze the organization of protein structures. The method only works from the contact probability matrix, i.e. the inter C{alpha}-distances translated into probabilities. It uses the principle of the conventional hierarchical clustering, leading to a series of nested partitions of the 3D structure. Every step aims at dividing optimally a unit into 2 or 3 sub-units according to a criterion called "partition index" assessing the structural independence of the sub-units newly defined. Moreover, an entropy-derived squared correlation R is used for assessing globally the protein structure dissection. The method is compared to other splitting algorithms and shows relevant performance.

Availability: An internet server with dedicated tools is available at http://www.ebgm.jussieu.fr/~gelly/.

{dagger}: deceased.
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This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J.-C. Gelly, C. Etchebest, S. Hazout, and A.G. de Brevern
Protein Peeling 2: a web server to convert protein structures into series of protein units.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W75 - W78.
[Abstract] [Full Text] [PDF]


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