Bioinformatique structurale

MOBI

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Modeling Biological macromolecules
Adresse

France

Description (English)

We study the structure, dynamics, and interactions of biological macromolecules using a range of molecular modeling tools, including structural bioinformatics and molecular simulations. We also develop our own  tools, both in the area of bioinformatics and in molecular simulations. Our ultimate goal is to better understand of the links between structure, interactions and, ultimately, biological functions at the molecular level. Our main activities focus on:

Biomembranes: structure, dynamics, and interactions

Biological membranes envelop and compartmentalize all living cells. Biomembranes are extremely dynamic entities at all levels – in fact the vast majority of them is liquid, in physiologically relevant states, which makes it very challenging to obtain structural information at high resolution with experimental techniques. We use molecular simulations at multiple levels, from quantum mechanics to all-atom and coarse-grained molecular dynamics simulations, to gain insight into membrane structure, dynamics, interactions, and transformations.

Protein-protein interactions

The main focus is on the prediction of protein-protein interactions (PPI), at the molecular level (assessment of docking methods) and at the cellular level (development of bioinformatics methods to predict PPI networks). The latter uses sequence similarity between a set of interacting proteins (reference PPI) and the proteins of the organism under scrutiny to infer interaction between its proteins.

SFBI
N'est pas membre de la SFBI

IMGT®

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
IMGT®, the international ImMunoGeneTics information system®
Adresse

34396 MONTPELLIER cedex 5 FRANCE
France

Téléphone
33(0)434359965
Fax
33(0)434359901
Description (English)

IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université Montpellier 2 and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

English keywords
immunogenetics, immunoinformatics, IMGT-ONTOLOGY, antibody, T cell receptor, IMGT Collier de Perles, major histocompatibility
SFBI
Membre de la SFBI

DMMP

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Dynamique des membranes et manteaux protéiques
Adresse

Institut de Pharmacologie Moléculaire et Cellulaire (IPMC)
660 Route des Lucioles
SOPHIA ANTIPOLIS

06560 VALBONNE
France

Téléphone
04 93 95 77 69
Fax
04 93 95 77 08
Description (English)

Various proteins remodel the membranes of organelles involved in intracellular transport. Protein coats deform membranes to promote the budding of vesicles. Golgins, sort of molecular strings, tether vesicles to restrict their diffusion. Lipid transporters adjust the membrane composition. Although very different, most of these mechanisms are controlled by small G proteins of the Arf family and by the physical chemistry of membranes.

We study these mechanisms through molecular, cellular and in silico approaches. With original assays based on fluorescence and light scattering, we follow elementary reactions such as the assembly cycle of protein coats, the tethering of liposomes by a golgin or the transfer of lipids. With fluorescence light microscopy and electron microscopy, we visualize these events in cells and in reconstituted systems. With molecular dynamics, we describe at the atomic level how specific protein motifs sense the chemistry and curvature of lipid membranes.

Recent Findings:

- Intracellular transport of cholesterol through the counter exchange of a phosphoinositide and its hydrolysis.
- Phospholipids with omega 3 acyl chains boost membrane deformation and fission
- Atomic description of the packing of lipids in membranes of various curvature and composition

HELIQUEST: a bioinformatics tools to analyze amphipathic helices with specific properties and search for sequences with similar properties (amino-acid composition, hydrophobic moment...).

SFBI
Membre de la SFBI

SaAB

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Statistiques et Algorithmique pour la Biologie
Adresse

Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT)
Inra
Chemin de Borde Rouge
BP 52627

31326 CASTANET-TOLOSAN cedex

France

Téléphone
0561285074
Fax
0561285335
Description (English)

The team develops mathematical, statistical and computational methods to address life science research problems. These methods are usually directly made available to biologists through dedicated software.

Bioinformatics problems addressed

The topics addressed in the team concern the localization and identification of functional elements in bacterial, plant and animal genomes. Three investigation levels are considered.     

  • Genetical level A genome is essentially seen through molecular markers whose locations on a chromosome are highly informative in genetics investigation. Localizing these markers on the chromosomes (genetic mapping and radiated hybrid mapping: Carthagène) in order to subsequently locate the regions linked to quantitative traits of interest (disease resistance, yield ...) with respect to those markers (QTL or quantitative trait loci localization by analyzing allelic transmission: MCQTL and by modelling linkage disequilibrium: HAPim). These QTLs can then be used in selecting varieties that combine several desirable traits.
  • Molecular level At the molecular level, the DNA sequence of the genome is directly analyzed to decode and identify functional regions in the sequence. These may be genes coding for proteins (in bacterial genomes and EST cclusters FrameD or in eukaryotic genomes: EuGène) or non coding genes corresponding to functional RNAs (MilPat, DARN!, ApolloRNA, RNAspace). The comparison of genomes of different species and identification of key events that separate them (recombination) can enable the transfer of information between genomes.
  • Gene expression level The use of DNA microarrays allows to partially observe the cellular activity at a given time. It is then possible to establish a link between the contextual conditions of the cell at observation time (disease, polluted environment) and the genes that are over (or under) expressed. This link may help trace the genes related to disease or allow for a diagnosis.

To go beyond the localization of isolated functional elements, we are are now increasingly interested in approaches aiming at the inference of gene regulatory networks. We are currently studying the simultaneous analysis of expression data and polymorphism data (such as SNP) on a collection of individuals. This allows to observe different perturbated modes of operation of the network to better infer gene network structures.

English keywords
genetical and radiated hybrids mapping, QTL mapping, sequence annotation, ncRNA search, inference of gene regulatory network
SFBI
Membre de la SFBI

ESF-RCPG

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Evolution, Structure et Fonction des RCPG
Adresse

Laboratoire MITOVASC
UMR CNRS 6214 - INSERM 1083
3 rue Roger Amsler

49100 ANGERS

France

Téléphone
0244688262
SFBI
Membre de la SFBI

ABI

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Atelier de BioInformatique
Adresse

75005 Paris
France

Téléphone
01 40 79 48 09
English keywords
bioinformatics, structural bioinformatics, génomic analysis, population genetics
SFBI
Membre de la SFBI

MTi

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Molécules à vocation Thérapeutique par approches In silico
Adresse

INSERM UMR-S 973
35 rue H. Brion

75205 Paris Cedex 13
France

English keywords
Structural bioinformatics, chemoinformatics, in silico screening, molecular modeling, peptide and protein structure
SFBI
Membre de la SFBI