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FRENCH INFRASTRUCTURE FOR INTEGRATED STRUCTURAL BIOLOGY

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CBS

STRUCTURAL BIOINFORMATICS

The CBS provides access to a unique set of web-servers and methodologies dedicated to structural bioinformatics and chemoinformatics. It is designed to provide detailed sequence-structure-function studies of proteins that have been identified as potential targets for structural biology studies. It includes:

(i) Identification of (distantly)-related 3D structures through fold-recognition techniques

(ii) Prediction of domain organization and delineation of domain boundaries

(iii) comparative 3D structure modeling

(iv) Ligand binding site predictions and focused comparative ligand docking in order to provide clues for prediction of potential functions.

The analysis is performed using dedicated software tools, many of them specifically developed by the CBS bioinformatics platform (e.g.: @TOME-2, PAT, ...).

It also take advantage of other software pipelines (e.g.: PipeAlign@IGBMC) to search for close homologues of the protein queries to refine sequence-structure alignment and sequence-structure-function relationships.

The target characterization facility offers two modes of access:

     1.  The user supplies the primary sequence and an e-mail address and the platform provides complete sequence-structure-function data in a dedicated format.

     2.  The user can ask for a rapid or thorough analysis to the platform staff.

Methodology development:

Gracy & Chiche,BMC Bioinformatics. 2010, 11:535.

Pons & Labesse,Nucleic Acids Res. 2009, W485-91.

Application studies:

Vigneronet al., Mol. Cell. Biol.,2011

Huanget al., P. N. A. S.,2011

Devices:

-interface Web: 4 Quadri-Core AMD Opteron, 16 Go of memory, 4 To of storage disk.

- Computation server: 16-node multi-cpu with 2 Go of memory per node.