research

Projects formerly developed at IGS-CNRS

Normal mode analysis

Docking - In Silico screening

  • GFscore is a methodology to accelerate the process of High Throughput Screening (HTS). We have extended the principle of consensus scoring by using a Non-Linear Neural Network approach. This GFscore global scoring function is a combination of the five scoring functions from in the Cscore package from Tripos Inc.
    Click here to submit a job to the GFscore web-server
    Collaboration with Xavier Morelliand Stéphane Betzi.
    REF: Betzi et al., J. Chem. Inf. Model., 2006

Mimivirus genome analysis

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Mimivirus genome analysis

  • CaMBOT probing led to the isolation of a novel calmodulin binding protein cmbB in the social amoeba Dictyostelium discoideum. Structural and bioinformatic analyses reveal that the cmbB protein is almost entirely comprised of tandem repeats of an IP22 motif, which is a more precise representation of the previously identified FNIP repeat. cmbB also appears to share structural homology to YopM, from the plague bacterium Yersenia pestis, and its closest homologues are found in Mimivirus.
  • Collaboration with Prof. Danton O'Day.
  • REF: O'Day et al., BBRC, 2006.



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PhydBac - phylogenomic display of bacterial genes



 

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CaspR: Automated molecular replacement using homology modelling

  • CaspR is a web-server for automated molecular replacement by screening a large number of homology models for a potential solution.
  • The method that is implemented in CaspR was first used to solve the crystal structure of the E. coli protein YecD (PDB-id 1J2R).
  • The implementation of this method as a web-based server is part of the PhD research work of Jean-Baptiste Claude
  • REF: Claude et al., NAR, 2004.
 

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3D-Coffee: multiple sequence-structure alignments with T-Coffee

 

 

 

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CaspR: Automated molecular replacement using homology modelling

 

 

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Structural biology

 

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FusionDB - a database of prokaryotic gene fusion events

 

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Genomic correlates of hyperthermostability

  • Statistical (principal component) analysis of the amino acid composition of most sequenced bacterial genomes. We show that the CHA-POL criteria (replacement of polar by charges residues in thermophilic organisms) is an optimal criteria to discriminate meso-philic from thermophilic proteins.
  • REF: Suhre and Claverie, J. Biol. Chem., 2003
 

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Bacterial genome sequencing and annotation

 

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