A5009109452- Protein Structure and Dynamics
- Hepatitis C virus research
- Genomics and Phylogenetic Studies
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Hepatitis B Virus Studies
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Genetics, Bioinformatics, and Biomedical Research
- ATP Synthase and ATPases Research
- Animal Virus Infections Studies
- Monoclonal and Polyclonal Antibodies Research
- Viral gastroenteritis research and epidemiology
- Advanced Proteomics Techniques and Applications
- Liver Disease Diagnosis and Treatment
- Distributed and Parallel Computing Systems
- Bacterial Genetics and Biotechnology
- DNA and Nucleic Acid Chemistry
- Cell Adhesion Molecules Research
- Mass Spectrometry Techniques and Applications
- Virus-based gene therapy research
- Mitochondrial Function and Pathology
- Algorithms and Data Compression
- Bacteriophages and microbial interactions
- Drug Transport and Resistance Mechanisms
Université Claude Bernard Lyon 1
2006-2021
Centre National de la Recherche Scientifique
2005-2020
Biologie Tissulaire et Ingénierie Thérapeutique
2016-2020
École Normale Supérieure de Lyon
2014
Structural and Molecular Basis of Infectious Systems
2011-2013
AgroParisTech
2011
Institut de Biologie et de Chimie des Protéines
2000-2009
Bipar
2009
Université de Lyon
2009
King's College Hospital NHS Foundation Trust
2008
Recently a new method called the self-optimized prediction (SOPM) has been described to improve success rate in of secondary structure proteins. In this paper we report improvements brought about by predicting all sequences set aligned proteins belonging same family. This improved SOPM (SOPMA) correctly predicts 69.5% amino acids for three-state description (alpha-helix, beta-sheet and coil) whole database containing 126 chains non-homologous (less than 25% identity) Joint with SOPMA neural...
Abstract Geno3D (http://geno3d-pbil.ibcp.fr) is an automatic web server for protein molecular modelling. Starting with a query sequence, the performs homology modelling in six successive steps: (i) identify homologous proteins known 3D structures by using PSI-BLAST; (ii) provide user all potential templates through very convenient interface target selection; (iii) perform alignment of both and subject sequences; (iv) extract geometrical restraints (dihedral angles distances) corresponding...
An algorithm has been developed to improve the success rate in prediction of secondary structure proteins by taking into account predicted class proteins. This method called 'double method' and consists a first from new which uses parameters type described Chou Fasman, their amino acid composition. These two independent predictions allow one optimize calculated over database provide final structure. tested on 59 (i.e. 10,322 residues) yields 72% prediction, 61.3% residues correctly for three...
A new method called the self-optimized prediction (SOPM) has been developed to improve success rate in of secondary structure proteins. This checked against an updated release Kabsch and Sander database, 'DATABASE.DSSP', comprising 239 protein chains. The first step SOPM is build sub-databases sequences their known structures drawn from 'DATABASE.DSSP' by (i) making binary comparisons all (ii) taking into account structural classes second submit each sub-database a using predictive algorithm...
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in Protein Data Bank (PDB) have not all been obtained using latest experimental computational methods. In this study a method is presented for automated re-refinement of existing structure models PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved terms fit to deposited X-ray data as well geometric quality....
We have developed a specialized database, HBVdb (http://hbvdb.ibcp.fr), allowing the researchers to investigate genetic variability of Hepatitis B Virus (HBV) and viral resistance treatment. HBV is major health problem worldwide with more than 350 million individuals being chronically infected. an enveloped DNA virus that replicates by reverse transcription RNA intermediate. genome optimized, circular encoding four overlapping reading frames. Indeed, each nucleotide takes part in coding at...
A graphic program has been developed to calculate the secondary structure content of proteins from their circular dichroism spectrum. All information concerning analysis and results are given on a single screen. The actual theoretical spectra plotted allow visual inspection fit quality. percentages statistical parameters (r. m. s., residuals) provided. is fully interactive for analysis. Moreover, cursors driven by mouse or arrow keys moveable onto yielding all wavelength, such as...
ABSTRACT Chronic hepatitis C virus (HCV) infection is a major cause of liver disease. The HCV polyprotein contains hypervariable region (HVR1) located at the N terminus second envelope glycoprotein E2. strong variability this 27-amino-acid due to its apparent tolerance amino acid substitutions together with selection pressures exerted by anti-HCV immune responses. No specific function has so far been attributed HVR1. However, presence surface viral particle suggests that it might be involved...
Abstract An innovative bioinformatic method has been designed and implemented to detect similar three‐dimensional (3D) sites in proteins. This approach allows the comparison of protein structures or substructures detects local spatial similarities: this is completely independent from amino acid sequence backbone structure. In contrast already existing tools, basis for a representation structure by set stereochemical groups that are defined independently notion acid. efficient heuristic...
The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad quasispecies within given host. A database allowing researchers investigate genetic structural variability all available HCV sequences is an essential tool for studies on molecular virology pathogenesis as well drug design vaccine development. We describe here European Hepatitis Virus Database (euHCVdb,...
Membrane proteins are estimated to represent about 25% of open reading frames in fully sequenced genomes. However, the experimental study remains difficult. Considerable efforts have thus been made develop prediction methods. Most these were conceived detect transmembrane helices polytopic proteins. Alternatively, a membrane protein can be monotopic and anchored via an amphipathic helix inserted parallel way interface, so-called in-plane (IPM) anchors. This type anchor is still poorly...
In October 2004, an expert meeting was convened in parallel with the 11th Symposium on Hepatitis C and Related Viruses to discuss how HCV sequence databases could introduce facilitate a standardized numbering system for nucleotides, proteins epitopes. Inconsistent inaccurate of locations DNA protein sequences is problem scientific literature. Consistency increasingly required functional clinical studies HCV. For example, unambiguous method referring amino acid substitutions at specific...
Collagens are thought to represent one of the most important molecular innovations in metazoan line. Basement membrane type IV collagen is present all Eumetazoa and was found Homoscleromorpha, a sponge group with well-organized epithelium, which may first stage tissue differentiation during animal evolution. In contrast, spongin seems be demosponge-specific collagenous protein, can totally substitute an inorganic skeleton, such as well-known bath sponge. freshwater Ephydatia mülleri, we...
Abstract Motivation ALIGNSEC is a module within ANTHEPROT designed for the interactive display, edition and printing of large-scale multiple alignments integrating secondary structure predictions. Availability implementation The part package (http://antheprot-pbil.ibcp.fr) which can be used freely academic users. It running on Windows Operating systems. For commercial use, please contact author.
On the basis of theoretical structural and comparative studies various avian leukosis virus SU (surface) envelope proteins, we have identified four small regions (I, II, III, IV) in their receptor-binding domains that could potentially be involved binding to receptors. From gene an subgroup A, constructed a set mutants which these were replaced by coding sequence FLA16, 16-amino-acid RGD-containing peptide known target for several cellular integrin Helper-free retroviral particles carrying...
We provide the scientific community with a web server which gives access to SuMo, bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins. SuMo is based on unique representation macromolecules using selected triplets chemical groups having their own geometry and symmetry, regardless restrictive notions main chain lateral chains amino acids. The heuristic extracting similar sites was used drive two major large-scale approaches. First, searching...