Structure Content

The ARIAweb server provides access to the main ARIA software functionalities (NMR data conversion and structure calculation). In addition, structure calculation results can be easily visualised, with a dedicated molecular viewer and graphical displays […]

We designed a continuous-flow culture system in which biofilm formation can be reproducibly monitored and controlled in microfermentors handled at flow-rates avoiding accumulation of planktonic bacteria. This model is suited for biofilm macroscopic analysis, […]

CapsuleFinder is a program that detects capsule systems with high accuracy in proteic sequences.  It is based on the use of HMM profiles for the detection of the essential proteins of capsule biogenesis and  requires computational models describing […]

Warning: This data is old and the site will be discontinued soon. We are working on an alternative. This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 […]

We have recently developed tools to visualize the results of CRISPR screens and design novel guide RNA for use in bacteria. These tools are available at crispr.pasteur.fr .

Find David Bikard Lab Plasmids

We originally developed genetic tools to study adhesion and biofilm formation in commensal and pathogenic E. coli species. These tools are made freely available to the scientific community upon request. • pKOBEG Lambda Red […]

The genomic and nomenclature databases of strains of pathogenic bacterial species are available through the Institut Pasteur BIGSdb portal: http://bigsdb.pasteur.fr. The portal is powered by the Bacterial Isolates Genome Sequence DataBase (BIGSdb) tool developed […]

HARIBOSS is a database of RNA-small molecules structures retrieved from the PDB database. HARIBOSS is regularly updated with all the structures resolved by X-ray, NMR, and cryo-EM, in which ligands with drug-like properties interact […]

We developed a clinically relevant in vivo model of catheter-associated biofilm infections to design new and efficient biofilm-eradication approaches applicable to contaminated totally implantable venous access port (TIVAP) catheters.      Key publications •  Chauhan, A., J.M. […]

In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary […]

We are currently developping new optogenetic tools of interest for System Neuroscience.  Optogenetics is the combination of genetics and optics to control well-defined events within specific cells of living tissue. It includes the discovery and insertion into cells […]

PLUMED-NEST is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper. Furthermore, PLUMED-NEST […]

CRISPR polymorphism is a powerful tool to subtype Salmonella strains and is now used in routine for epidemiological investigations. This tool gets a CRISPR profile by identifying the presence of known spacers and direct […]

Warning: This data is old and the site will be discontinued soon. We are working on an alternative. Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial […]

Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification […]

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are […]

The database TXSSdb includes all results from our works on the detection of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. It is by far the most complete database […]