Serge A. Hazout

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By using an unsupervised cluster analyzer, we have identified a local structural alphabet composed of 16 folding patterns of five consecutive C(alpha) ("protein blocks"). The dependence that exists between successive blocks is explicitly taken into account. A Bayesian approach based on the relation protein block-amino acid propensity is used for prediction(More)
Two efficient algorithms have been developed which allow amino acid side chain conformations to be optimized rapidly for a given peptide backbone conformation. Both these approaches are based on the assumption that each side chain can be represented by a small number of rotameric states. These states have been obtained by a dynamic cluster analysis of a(More)
Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated, or replaced by zero or estimated by the k-Nearest(More)
Three-dimensional protein structures can be described with a library of 3D fragments that define a structural alphabet. We have previously proposed such an alphabet, composed of 16 patterns of five consecutive amino acids, called Protein Blocks (PBs). These PBs have been used to describe protein backbones and to predict local structures from protein(More)
The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decomposed into a series of short segments defined by their inter-alpha-carbon distances. Basically, the model takes into account the sequentiality of the(More)
Knowledge of the disulfide bonding state of the cysteines of proteins is of major interest in designing numerous molecular biology experiments, or in predicting their three-dimensional structure. Previous methods using the information gained from aligned sets of sequences have reached up to 82% of success in predicting the oxidation state of cysteines. In(More)
We have studied the effect of backbone inaccuracy on the efficiency of protein side chain conformation prediction using rotamer libraries. The backbones were generated by randomly perturbing the crystallographic conformation of 12 proteins and exhibit C alpha r.m.s.d.s of up to 2 A. Our results show that, even for a perturbation of the backbone fully(More)
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.(More)
The frequencies of DF508, the main cystic fibrosis mutation, vary among different populations in Western Europe; they are higher in northwestern Europeans than in southeastern populations. Our new analysis is based on results from 66 different laboratories on 17,886 cystic fibrosis chromosomes (from 70 locations and 26 countries). The correlation between(More)
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(More)