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Volume 5


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In Silico Biology 5, 0026 (2005); ©2005, Bioinformation Systems e.V.  



New assessment of a structural alphabet

Alexandre G. de Brevern

Equipe de Bioinformatique Génomique et Moléculaire (EBGM), INSERM U 726, Université Denis DIDEROT - Paris 7, case 7113, 2, place Jussieu, 75251 Paris, France
Phone: +33-1 44 27 77 31,  Fax: +33-1 43 26 38 30
Email: debrevern@ebgm.jussieu.fr




Edited by E. Wingender; received December 23, 2004; revised and accepted February 21, 2005; published March 16, 2005


Abstract

A statistical analysis of the Protein Databank (PDB) structures had led us to define a set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one defined by the (Φ, Ψ) dihedral angles of 5 consecutive residues. Here, we analyze the effect of the enlargement of the PDB on the PBs' definition. The results highlight the quality of the 3D approximation ensured by the PBs. These last could be of great interest in ab initio modeling.

Keywords: secondary structure, structure-sequence relationship, ab initio modeling