Workshop bioinformatics biology formation.pdf

Bioinformatics

1. Workshop 5-6
B cell/ T cellepitope
database
tools.iedb.org
Presented by:
Dr ABID G.
Dr ILIAS W.
2023/2024

2. Workshop objectives
•1. What is a B cell/T cell epitope?
•2. Exploring IEDB database and the different
prediction tools on IEDB
•3. Linear sequence-based epitope prediction
methods
•4. Discontinuous 3D structure-based epitope
prediction methods

3. B cell/ T cellepitope
https://www.creative-biolabs.com/drug-discovery/therapeutics/b-cell-epitope-prediction.htm
More than 90% of B cell
epitopes are estimated to
be discontinuous
Barlow et al, Nature. 1986.

5. Is itlinearor
discontinued?

7. Minimal Criteriafor Epitope Inclusion
•Linearpeptide <50 aminoacidsin length
•Testedas an immunogenor an antigen
•Non-peptidicepitopes<5,000 Daltons
•Minimal information required(sequence, outcome, host, etc.)

8. Immune Epitope Database
Overview

10. LiteratureCuration

11. Fromwhereall thesedata?
•Consistent data entry requires ------->well
defined data structure -------> A Database of
Experiments

12. Collaborations withOntologies
•Providesstandardizednomenclature, definitions,
•synonyms, and hierarchicalrelationships
•Makescuration easier
•Enhancesuser experience
•Ensuresconsistencyand accuracy

13. Exemples

14. Exemples

26. When should I do epitope prediction
➢You have verified thoroughly
that no information is
available in the IEDB on the
antigen of your interest
➢You want to know all the
candidate antigenic
determinants in an antigen of
your interest other than
epitopes provided in the IEDB

27. Types of B Cell Epitope Prediction
Sequence-based epitope
prediction
Structure-based epitope
prediction
• 3D solved structure or
structural model of antigen is
not required
• Relies on prediction methods
for surface accessibility
• 3D solved structure or
structural model of antigen is
available
• Surface accessibility and
secondary structure are known
BepiPred
method
DiscoTope
method

29. Sequence-based epitope prediction

34. Structure-basedEpitope Prediction

44. •On IEDB, perform a research on epitopes of SARS-COV 2 virus (Beta
variant) infecting Human and causing infection disease.
•How many epitopes are there in this databases?
•How many antigen are there, name these antigen?
•give the range of positions in which these epitopes are found on the antigen
•How many antigen receptors are there , on witch type of cell are they
found?
•Choose the epitopewiththe followingID 2116335, isita linearor
discontinioudepitope? How manytimes itwasstudiedand tested?
•Retrievethe 3D strucutureof thisepitope.
Practice Exercise 1

45. •Use BepiPredand DiscoTopeto predictB cellepitopesof dengue 2 virus
envelopeglycoprotein
•Downloadcrystalstructure and sequenceof dengue 2 virus envelope
glycoproteinfromPDB (PDB ID: 4UTC)
Practice Exercise 2