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

The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited

Free-Standing DNA Origami Superlattice to Facilitate Cryo-EM Visualization of Membrane Vesicles

Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes

Phosphorylation of the F-BAR protein Hof1 drives septin ring splitting in budding yeast

1H, 13C and 15N backbone and side-chain resonance assignments of the human oncogenic protein NCYM

Development of new approach methods for the identification and characterization of endocrine metabolic disruptors-a PARC project

1H, 13C and 15N backbone and side-chain resonance assignments of the human oncogenic protein NCYM

Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software

Emergence of slip-ideal-slip behavior in tip-links serve as force filters of sound in hearing

Increases in cyclin A/Cdk activity and in PP2A-B55 inhibition by FAM122A are key mitosis-inducing events

pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging

LactoSpanks: A Collection of IPTG Inducible Promoters for the Commensal Lactic Acid Bacteria Lactobacillus gasseri

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins

An innovative in situAFM system for a soft X-ray spectromicroscopy synchrotron beamline

Critical micellar concentration determination of pure phospholipids and lipid-raft and their mixtures with cholesterol

Cancer selective cell death induction by a bivalent CK2 inhibitor targeting the ATP site and the allosteric alphaD pocket

Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds

Development of HC-258, a Covalent Acrylamide TEAD Inhibitor That Reduces Gene Expression and Cell Migration

The genome of a bunyavirus cannot be defined at the level of the viral particle but only at the scale of the viral population

A single-domain intrabody targeting the follicle-stimulating hormone receptor impacts FSH-induced G protein-dependent signalling

Structure-function relationships in protein homorepeats

3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

wTSA-CRAFT: an open-access web server for rapid analysis of thermal shift assay experiments

Development of LM-41 and AF-2112, two flufenamic acid-derived TEAD inhibitors obtained through the replacement of the trifluoromethyl group by aryl rings

Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae

Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria

Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction

The novel cyclophilin inhibitor C105SR reduces hepatic ischaemia-reperfusion injury via mitoprotection

Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies

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