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

Abstract : 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 Calpha-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/
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https://www.hal.inserm.fr/inserm-00133725
Contributor : Alexandre G. de Brevern <>
Submitted on : Tuesday, February 27, 2007 - 3:26:51 PM
Last modification on : Tuesday, November 3, 2020 - 11:18:02 AM
Long-term archiving on: : Friday, November 25, 2016 - 3:03:56 PM

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Jean-Christophe Gelly, Alexandre de Brevern, Serge Hazout. 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.. Bioinformatics, Oxford University Press (OUP), 2006, 22 (2), pp.129-33. ⟨10.1093/bioinformatics/bti773⟩. ⟨inserm-00133725⟩

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