1. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Project in Immunological Bioinformatics Morten Nielsen, CBS, BioCentrum, DTU

2. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Selection of epitopes Conservation Proteasome cleavage –Cleavage of C-terminus Tap binding MHC binding CTL binding/activation

3. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Prediction methods SYFPEITHI –Welcome to SYFPEITHIWelcome to SYFPEITHI Bimas –HLA Peptide Binding PredictionsHLA Peptide Binding Predictions

4. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU EasyPred Web interface for training of weight matrices and neural networks Weight matrices –Sequence weighting –Pseudo counts Neural networks –Hidden neurons –Splitting of Test/Training data –Cross validated training

5. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Weight matrices Is some pattern hidden in the sequences that binds MHC? –First step is to select peptides from the data pool that bind MHC –Next use the methods of sequences weighting and pseudo counts to estimate the weight matrix Evaluate the accuracy of the matrix on an independent data set.

6. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Evaluation of prediction accuracy True positive proportion = TP/(AP)False positive proportion = FP/(AN) A roc =0.5 A roc =0.8 Roc curves Pearson correlation TPFP AP AN

7. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU MHC peptide binding affinities Transformation o = 1 - log(aff nM)/log(50000) High binder aff < 50nM => o > 0.638 Intermediate binder aff < 500nM => o > 0.426

8. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Test/Training performance Test max 20% 80% Test TRain

9. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU 5 fold test/training 20%

10. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Your favorite protein Swiss-Prot –http://us.expasy.org/sprot/ Sars sequence –Sars entrySars entry

11. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Combination with Proteasomal cleavage Prediction of MHC binding 227 RLNQLESKV 0.620 223 LLLDRLNQL 0.589 352 ILLNKHIDA 0.461 131 IVWVATEGA 0.369 353 LLNKHIDAY 0.360 45 GLPNNTASW 0.274 113 YLGTGPEAS 0.271 304 QIAQFAPSA 0.270 407 QLQNSMSGA 0.263 166 TTLPKGFYA 0.249 161 QLPQGTTLP 0.246 104 ELSPRWYFY 0.234 394 TLLPAADMD 0.227 139 ALNTPKDHI 0.222 224 LLDRLNQLE 0.218 167 TLPKGFYAE 0.215 222 LLLLDRLNQ 0.213 RLNQLESKV S..SS http://www.cbs.dtu.dk/ Netchop prediction server

12. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Project plan Follow the project description in detail Write down detailed notes as you go through the project Aflever kort resultat summery tirsdag d. 27. April (1-2 sider) kl 13.00