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


BACKGROUND
An Internet server with dedicated tools is available at http://www.ebgm.jussieu.fr/~gelly/
Gelly
Jean-Christophe
JC
INSERM U726, Equipe de Bioinformatique Génomique and Moléculaire (EBGM), Université Denis Diderot-Paris 7, case 7113, 75251 Paris Cedex 05, France.
de Brevern
Alexandre G
AG
Hazout
Serge
S
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods*; D011487:Protein Conformation; D017510:Protein Folding; D021122:Protein Subunits; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D010446:Peptide Fragments; D021122:Protein Subunits; D011506:Proteins