WHO/TDR sponsored Training Course on 
‘Bioinformatics applied to tropical diseases'
 ICGEB, India (October, 2005)

Epitope Prediction

 25-10-2005 

Epitope prediction programs                                           

• Antigenic : Find antigenic sites in proteins (EMBOSS)
• SYFPEITHI - A DATABASE OF MHC LIGANDS AND PEPTIDE MOTIFS 
• Related Databases
• Antigenic determinants@VirGen
• Conformational Epitope Prediction Server @UoP

 Exercises                                                                       

• Retrieve the protein sequences of the following antigenic proteins from any of the public-domain databases. save sequences in FASTA format as text files. Predict the B-cell antigenic determinants. 

  • nucleocapsid protein N of SARS Coronavirus (strain Urbani)

  • matrix protein M of SARS Coronavirus (strain Urbani)

• Predict the anchor residues of the Predicted T-cell epitope (TDWSGYSGSFVQHPEL) that are likely to bind to H2-Kd using the SYFPEITHI database.

• PDB entry 1SVB is the structure of envelope glycoprotein of Tick-borne encephalitis virus. Predict the possible conformational epitopes using CEP server.

Ó Bioinformatics Centre, University of Pune (2005)