Serge A. Hazout

Learn 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)
UNLABELLED PredAcc is a tool for predicting the solvent accessibility of protein residues from the sequence at different relative accessibility levels (0-55%). The prediction rate varies between 70. 7% (for 25% relative accessibility) and 85.7% (for 0% relative accessibility). Amino acids are predicted in four categories: almost certainly hidden and almost(More)
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 (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to(More)
We have developed a new algorithm 'Complete sentences compatibility' (CSC) which uses single and double digestion fragments to rapidly determine restriction maps of circular DNA. From possible combinations of fragments of each simple digestion, which we call 'sentences of decomposition', we construct a restriction map which combines the sentences while(More)
MOTIVATION Complete genomic sequences will become available in the future. New methods to deal with very large sequences (sizes beyond 100 kb) efficiently are required. One of the main aims of such work is to increase our understanding of genome organization and evolution. This requires studies of the locations of regions of similarity. RESULTS We present(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)
MOTIVATION Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for SImilar Regions in Chromosomes' (ASSIRC; Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to(More)
MOTIVATION Molecular evolution, which is classically assessed by comparison of individual proteins or genes between species, can now be studied by comparing co-expressed functional groups of genes. This approach, which better reflects the functional constraints on the evolution of organisms, can exploit the large amount of data generated by genome-wide(More)
UNLABELLED MOSAIC is a set of tools for the segmentation of multiple aligned DNA sequences into homogeneous zones. The segmentation is based on the distribution of mutational events along the alignment. As an example, the analysis of one repeated sequence belonging to the subtelomeric regions of the yeast genome is presented. AVAILABILITY Free access from(More)