Imitating the immune system

March 23, 2007
Claus Lundegaard | Immunological Bioinformatics, CBS, Technical University of Denmark

At CBS, we have during the recent years developed a number of web tools to be used in immunological research. These tools are all linked at http://www.cbs.dtu.dk/services and include a predictor of proteasomal cleavage; NetChop-3.0 [1], a predictor of MHC class I peptide binding; NetMHC-3.0, the algorithms are described in [2,3], a CTL-epitope predictor; NetCTL-1.2 [4], a tool predicting linear B-cell epitopes; BebiPred, [5], a platform for prediction of discontinuous B-cell epitopes, DiscoTope, [6], and a tool for analysis of human immunoglobulin VDJ recombination; VDJsolver [7]. All methods have been validated in large-scale benchmark calculations and compete all with the state of the art prediction methods. Furthermore, we have developed some bioinformatics web-tools, which are very useful in immunological studies, including a general motif predictor; EasyGibbs (http://www.cbs.dtu.dk/biotools/EasyGibbs) that are usable for, e.g., MHC class II binding-motif recognition [3], and a visualization tool for linear epitopes; Epiplot (http://www.cbs.dtu.dk/services/Epiplot-1.0). All the tools are freely accessible over the Internet using any major web-browser. I would like to use this opportunity to go through some os the latest developments in the prediction algorithms behind these tools.

Speaker Details

1993: MSc. Biochemistry.1998: Ph.D, Protein Chemistry.Thesis title: Kinetic Properties of Pyrimidine Phosphoribosyltransferases and Sequence Analysis of Type 1 Phosphoribosyltransferases1998-2002: Computational Scientist, Structural Bioinformatics Advanced Technology, Denmark, a subsidiary of Structural Bioinformatics, Inc. (SBI), San Diego, Ca.Fundamental research in local structure prediction and automatic algorithms of homology modelling and fold recognition.2002: Scientific consultant, Plexus Vaccines, Inc., San Diego, Ca.2002-2004: Assistant professor, Immunological Bioinformatics, CBS, Technical University of Denmark.2004-: Associated professor, Immunological Bioinformatics, CBS, Technical University of Denmark.Development of epitope dicovery algorithms