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Bioinformatics Vol. 19 no. 3 2003
Pages 345-353
© 2003 Oxford University Press

JOBIM Paper

‘Hybrid Protein Model’ for optimally defining 3D protein structure fragments

A.G. de Brevern * and S. Hazout

Equipe de Bioinformatique Génomique et Moléculaire, INSERM U436, Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris cedex 05, France

Received on February 1, 2002 ; revised on June 6, 2002 ; accepted on September 9, 2002

Motivation: Our aim is to develop a process that automatically defines a repertory of contiguous 3D protein structure fragments and can be used in homology modeling. We present here improvements to the method we introduced previously: the ‘hybrid protein model’ (de Brevern and Hazout, Theor. Chem. Acc., 106, 36–47, (2001)) The hybrid protein learns a non-redundant databank encoded in a structural alphabet composed of 16 Protein Blocks (PBs; de Brevern et al., Proteins, 41, 271–287, (2000)). Every local fold is learned by looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position corresponds to a cluster of similar 3D local folds.

Results: In this paper, we describe improvements to our method for building an optimal hybrid protein: (i) ‘baby training,’ which is defined as the introduction of large structure fragments and the progressive reduction in the size of training fragments; and (ii) the deletion of the redundant parts of the hybrid protein. This repertory of contiguous 3D protein structure fragments should be a useful tool for molecular modeling

Contact: debrevern{at}urbb.jussieu.fr

* To whom correspondence should be addressed.


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