Accueil > Research > Research groups > Methods and Electron Microscopy Group (G.Schoehn) > Pellequer Team > Structural Bioinformatics
Structural BioinformaticsStructural bioinformatics is tools and methods allowing the prediction, characterization, and analysis of sequences and structures of macromolecules. |
Adepth : A method to compute the depth of atoms in proteins.We applied the signed distance function (SDF) for representing the depths of atoms in a macromolecule. The calculations of SDF values were performed on grid points in a rectangular box that accommodates the macromolecule. The depth for an atom inside the molecule was then obtained as a result of tri-linear interpolation of SDF values at the nearest grid points surrounding the atom. Adepth allows you to :
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BridgeD : Prediction of the optimal insertion site of a disulfide bridge in a protein.There are three major reasons why the insertion of disulfide bridges into a protein is important :
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Destripe : A method to eliminate stripe noise from AFM images.We have developed a stripe noise reduction protocol, called DeStripe, for single biomolecule images obtained by AFM that are contaminated by heavy and thin bands of vertical noise. To detect and restore noisy pixel, the program adopts a "divide and conquer" strategy by dividing the Fourier spectrum of the image into a central region and a peripheral region. The method is also applicable to other noisy images with high density bands such as those acquired by scanning electron microscopy. The noise reduction effect introduced by DeStripe allows for better visualization of objects without introducing additional artifacts into the restored image. Example of image processing : Raw image__________________Denoised image____________Noise image |
Bepitope : Software for predicting B-cell epitopesBepitope is a computer tool for predicting the antigenic sites of a protein. Odorico M. and Pellequer J.-L. (2003) BEPITOPE : predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recognit. 16 : 20-22. A modern version of the original PREDITOP tool : Pellequer J-L and Westhof E (1993) PREDITOP : a program for antigenicity predictions. J. Mol. Graph. 11 : 204-210. An antigenic site is the region of a protein that is / will be recognized by an antibody molecule. The goal of Bepitope is to identify the antigenic sites of a protein that will tend to adopt the same cognate 3D structure once synthesized as a peptide. The new online version of Bepitope is here >>>>>>>>>>>>> : bepitope.ibs.fr A tutorial will be provided soon. |