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Bioinformatics Advance Access originally published online on November 14, 2005
Bioinformatics 2006 22(2):129-133; 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{at}oxfordjournals.org

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

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

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

*To whom correspondence should be addressed.

Motivation: The object of this study is to propose a new method to identify small compact units that compose 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 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 subunits according to a criterion called ‘partition index’ assessing the structural independence of the subunits 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/

Contact: debrevern{at}ebgm.jussieu.fr.

Received on September 2, 2005; revised on October 19, 2005; accepted on November 8, 2005

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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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