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  • Title: 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.
    Author: Gelly JC, de Brevern AG, Hazout S.
    Journal: Bioinformatics; 2006 Jan 15; 22(2):129-33. PubMed ID: 16301202.
    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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