Tools

Software ABCIS

All
Y Sequence Analysis
Y Structure Modeling
Z Ligand Interaction

PAT

Protein Analysis Toolkit for integrated biocomputing on the web.
Jerome Gracy and Laurent Chiche (2005), Nucleic Acids ResearchWeb Server issue, 33, W65-71.

Additional Sponsors: ACI-IMPBio
- Y Sequence Analysis
- Y Structure Modeling
@TOME V3

Bioinformatics Tools Server, a pipeline for comparative modeling of protein-ligand complexes.
Pons JL & Labesse G.(2009) Nucleic Acids Research ; doi : 10.1093/nar/gkp368

Additional Sponsors : ACI-IMPBio
- Y Structure Modeling
- Z Ligand Interaction
TITO

A tool for incremental threading optimization in order to help alignment and molecular modeling at any sequence similarity level.
Labesse G. and Mornon JP, (1998) Bioinformatics14, 206-211
- Y Structure Modeling
VITO

An interactive tool for homology modelling and protein family study coupling a full featured alignment editor with a complete 3D viewer. ViTO has its own macro language.
Catherinot, V and Labesse, G.(2004) Bioinformatics20,3694-3696

Additional Sponsors : Inserm (AIGE)
- Y Structure Modeling
P-SEA

A program for secondary structure assignment from Ca
Labesse G., Colloc'h N., Pothier J. and Mornon J.-P., (1997)
CABIOS vol 13., no. 3, pages 291-295
- Y Structure Modeling
EvDTree

EvDTree creates structure-dependent substitution profiles based on decision tree classification of 3D environments.
Gelly, J.-C., Chiche, L. and Gracy, J. (2005), BMC Bioinformatics 6:4

Additional Sponsors : Action, Bioinformatique, Inter-EPST
- Y Structure Modeling
EDMON v3

Endocrine Disruptor MONitoring - A computational tool to study interactions between nuclear hormone receptors and endocrine-disrupting chemicals
Delfosse et al, PNAS, 2012 - Doi : 10.1073/pnas.1203574109

Additional Sponsors : ANR BISCOT
- Y Structure Modeling
- Z Ligand Interaction
CoSiAn

CoSiAn (Combinatorial Similarity Analysis)
Similarity analysis between a reference ligand and a bank of ligands to screen, using a combination of 2D and 3D similarity tools.

Victor Reys - Violaine Moreau - Gilles Labesse
- Y Structure Modeling
- Z Ligand Interaction
VITO2

An interactive online or local Java tool for homology modelling and protein family study coupling a full featured alignment editor with a complete 3D viewer.

Grand F, Pons JL, Labesse, G (2016)
- Y Structure Modeling

Database ABCIS

Atome database

Several genomes, databases, or protein family have been modeled during various studies with the help of automatic procedure of @TOME. The generated models are accessible from this database.

Reference : Pons JL & Labesse G.(2009) Nucleic Acids Research ; doi : 10.1093/nar/gkp368
Knottin database

This web server is dedicated to the protein structural family of Knottins
Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L. (2004) Nucleic Acids Res.;32(1):D156-9.
Postic G, Gracy J, Périn C, Chiche L, Gelly JC. (2018) Nucleic Acids Res.;46(D1):D454-D8.

Additional Sponsors : ACI-IMPBio

Admin.Resp.	Florence Lepage
	(33) 04 67 41 79 04

Admin.Resp.	Didier Debain
	(33) 04 67 41 79 01

Manager.Assist.	Marion Boutin
	(33) 04 67 41 79 04

Centre de Biologie Structurale

Latest publications

GEF14 acts as a specific activator of the plant osmotic signaling pathway by controlling ROP6 nanodomain formation

A mechanism for ligand-dependent activation of AHR

A two-in-one expression construct for biophysical and structural studies of the human pregnane X receptor ligand-binding domain, a pharmaceutical and environmental target

An abundant ginger compound furanodienone alleviates gut inflammation via the xenobiotic nuclear receptor PXR in mice

Cryo-EM structure and regulation of human NAD kinase

Binding-Site Switch for Protein Kinase CK2 Inhibitors

Binding-site switch of Protein Kinase CK2 inhibitors

APH Inhibitors that Reverse Aminoglycoside Resistance in Enterococcus casseliflavus

Efficient Biochemical Method for Characterizing and Classifying Related Amyloidogenic Peptides

Microbes Saving Lives and Reducing Suffering

Site-Specific Incorporation of Fluorinated Prolines into Proteins and their Impact on Neighbouring Residues

Measuring Bacterial Flagellar Motor Dynamics via a Bead Assay

Determining the Relative Affinity of ORPs for Lipid Ligands Using Fluorescence and Thermal Shift Assays

What Structural Biology Tells Us About the Mode of Action and Detection of Toxicants

Structural Insights Into Thyroid Hormone Receptors

Structural basis of orientated asymmetry in a mGlu heterodimer

Structure of the aminoterminal domain of the birnaviral multifunctional VP3 protein and its unexplored critical role

Microbial biosensors for diagnostics, surveillance and epidemiology: Today's achievements and tomorrow's prospects

Towards the design of ligands of the internal pocket TEADs C-terminal domain

Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins

Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies

Molecular model of a bacterial flagellar motor in situreveals a parts-list of protein adaptations to increase torque

The flavonoid resokaempferol improves insulin secretion from healthy and dysfunctional pancreatic beta-cells

Split Reporters Facilitate Monitoring of Gene Expression and Peptide Production in Linear Cell-Free Transcription-Translation Systems

A molten globule ensemble primes Arf1-GDP for the nucleotide switch

The TOPOVIBL meiotic DSB formation protein: new insights from its biochemical and structural characterization

A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication

Quantifying surface tension and viscosity in biomolecular condensates by FRAP-ID

A fully sequenced collection of homozygous EMS mutants for forward and reverse genetic screens in Arabidopsis thaliana

@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking

VITO2

Software ABCIS

Database ABCIS

CoSiAn

CBS Teams

Structure, Dynamics and Function of biomolecules by NMR

Structure and function of highly flexible proteins

Multi-scale structural biology

ABCIS

Nuclear Receptors as Integrators of Endogenous and Environmental Signals

Mechanisms of DNA Segregation and Remodelling

Physics and mechanics of biological systems

Integrative Biophysics of Membranes

Multiscale Biomolecular Modeling

Synthetic Biology

Chromosome structure and homologous recombination in meiosis

Functional and synthetic genomics

Structure and function of the aryl hydrocarbon receptor

Postdoctoral position – Team Integrative Biophysics of Membranes

Postdoctoral position – Team Integrative Biophysics of Membranes

Connexion