The complexity of the immune system dwarfs the complexity of genomic data by several magnitudes. Yet, the rational design of vaccines must be able to wade through this complexity to make highly effective vaccines with little side effects. In this presentation made at the Functional Genomics and Bioinformatics meeting of the East African Workshop, I discuss how exactly computers may aid in the rational design of vaccines.

1. Computer Aided Vaccine Design Geoffrey H. Siwo East Africa Regional Worshop 2007

13. Exogenous Antigen Processing

14. Endogenous Antigen Processing

16. Sites for MHC class I Epitope Prediction

22. The score of a peptide is calculated by summing up the individual scores Of the amino acids at each position.

23. Quantitative Matrices based Methods Tool URL Alleles Covered ProPred http://www.imtech.res.in/raghava/propred1 47 MHC alleles nHLAPred http://www.imtech.res.in/raghava/nhlapred 67 MHC alleles SYFPEITHI http://www.syfpeithi.de > 200 MHC alleles LpPEP http://reiner.bu.edu/zhiping/lppep.html 1 MHC allele RANKPEP http://mif.dfci.harvard.edu/Tools/rankpep. html >40 MHC alleles BIMAS http://bimas.dcrt.nih.gov/molbio/hla_bind/ >46 MHC alleles MAPPP http://reiner.bu.edu/zhiping/lppep.html >50 MHC alleles

26. General schema of Machine learning Approaches Dataset of MHC binding and non-binding peptides Training set Training of ANN or SVM validation Test set Prediction tool

28. MULTIPRED: Artificial Neural Network based Prediction