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Software and tools

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  • 1 Download
  • ABCIS
  • Crystallography
  • NMR
  • SAXS
  • Y Sequence Analysis
  • Y Structure Modeling
  • Z Ligand Interaction
  • 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
  • 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
  • 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
  • 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
  • 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 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
  • 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

    • Z Ligand Interaction
  • A Ligand Transposition Server : This server allows comparative docking of ligands into the ATP-binding site of a protein kinase (target)
    Martin L, Catherinot V, Labesse G.(2006) Nucleic Acids Research Web Server issue:34 W325-W329

    Additional Sponsors : La Ligue contre le cancer

    • Z Ligand Interaction
  • A Ligand Transposition Server : This server allows rapid selection of ligands fitting the active site of the submitted protein by superposition of its three-dimensional structure with those of known complexes of protein/ligands of the family.
    Martin L, Catherinot V, Labesse G.

    Additional Sponsors : La Ligue contre le cancer

    • Z Ligand Interaction
  • A graphical NMR assignment software.
    André PADILLA (CBS)

    • NMR
  • Consensus Rules for Amino-Acid Characterisation using a Kernel method (SVM).
    The spin system typing consensus is based on the following softwares : Rescue, RescueN, Rescue2, Platon, and one other using SVM algorithm.
    Benod C., Delsuc MA., Pons JL (2006) J. Chem. Inf. Model. 46 (3) 1517-1522

    Additional Sponsors : ACI-IMPBio

    • NMR
  • Adapting the Charge Flipping algorithm to biological macromolecule diffraction data :
    * ab initio determination of protein crystal structures at atomic resolution
    * heavy atom or anomalous scatterers substructure determination

    Dumas C. & van der Lee A. (2008) "Macromolecular structure solution by charge flipping", Acta Cryst D64, 864-873.

    Palatinus L. & Chapuis G. (2007) "SUPERFLIP, a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions", J. Appl. Cryst.40,786-790.

    • Crystallography
  • A protocol for the incorporation of selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli based on the use of a suitable cysteine auxotrophic strain.

    Strub MP., Hoh F., Sanchez JF., Strub JM., Böck A., Aumelas A. & Dumas C. (2003) "Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing", Structure , 11, 1359-1367.

    • Crystallography
  • This web 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. Jan 1 ;32(1):D156-9.

    Additional Sponsors : ACI-IMPBio

    • Y Sequence Analysis
  • Download area for data and tools developed at CBS

    • 1 Download
  • A protein-protein complex structure by SAXS and computational docking


    B Jiménez-García, C Pons, DI. Svergun, P Bernadó and J Fernández-Recio.
    Nucleic Acids Research 2015; doi: 10.1093/nar/gkv368

    • SAXS
  • Calculation of sequence specific protein solvent accessibilities in the unfolded ensemble

    Estrada, J., Bernadó, P., Blackledge, M., and Sancho, J. (2009). ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble. BMC Bioinformatics, 10, 104. URL


    Bernadó, P., Blackledge, M., and Sancho, J. (2006). Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles. Biophysical Journal, 91, 4536–4543. URL

    • Y Structure Modeling
  • Whole list of bioinformatic tools installed at CBS

    • ABCIS
  • Automatic detection of diffusion modes within biological membranes using backpropagation neural network

    Dosset P., Rassam P., Fernandez L., Espenel C., Rubinstein E., Margeat E. and Milhiet P.E. ( 2016 ) BMC Bioinformatics ( in press )

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