- Communication -

Volume 4

Full article

Local backbone structure prediction of proteins

Alexandre G. de Brevern¹*, Cristina Benros¹, Romain Gautier^1,2, Hélène Valadié^1,3, Serge Hazout¹ and Catherine Etchebest¹

¹ Equipe de Bioinformatique Génomique et Moléculaire (EBGM), INSERM E03-46, Université Denis Diderot - Paris 7, case 7113, 2, place Jussieu, 75251 Paris, France.
² Université Pierre & Marie Curie - Paris 6, 75005 Paris, France.
³ CEA, 17 avenue des Martyrs, 38054 Grenoble, France.
  Email: alexandre.debrevern@ebgm.jussieu.fr

*  corresponding author


Edited by E. Wingender; received April 13, 2004; revised and accepted May 26, 2004; published May 29, 2004

Abstract

A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (Φ, Ψ) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically.

Key words: structure prediction, confidence index, Bayesian approach