Roll immune-informatics · About the tool chosen:

Roll
No. 15081560-012

Assignment:
02

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Tools in
immune-informatics

·       
About the tool chosen: (IEDB analysis
resource Consensus tool)

This tool is
about the ability of epitope to bind with a specific MHC class-1 molecule.
Epitope is a location of an antigen which is recognized or identified by our
immune system. There may be a T- cell epitope and B-cell epitope (presented by
a MHC molecule) that are identified by T-cell receptors and B-cell receptors. The
IEDB selection gives us a chance to deal with a well-tested epitope associated
tools through a general web interface.

IEDB prediction
is a default selection method. This selection method is based on availability
of those who is going to predict and predictive performance. The selection uses
the best known method in which affinity of MHC molecule to epitope is
predicted. IEDB uses the CONSENSUS
method of ANN, SMM and combLib if corresponding predictor is available.

·        
Working:

1-     
First,
I selected an antigen (CD81 antigen).

2- I found the sequence
of protein’s amino acids. That is:

MGVEGCTKCIKYLLFVFNFVFWLAGGVILGVALWLRHDPQTTNLLYLELG
DKPAPNTFYVGIYILIAVGAVMMFVGFLGCYGAIQESQCLLGTFFTCLVI
LFACEVAAGIWGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTF
HETLDCCGSSTLTALTTSVLKNNLCPSGSNIISNLFKEDCHQKIDDLFSG
KLYLIGIAAIVVAVIMIFEMILSMVLCCGIRNSSVY

And the protein is CD81 antigen

The sequence is of 236 amino acids.

3- Then I uploaded this sequence in
protein sequence bar (in T-cell epitope prediction) in FASTA format.

4- Next, one sequence format was chosen.

5- The IEDB recommended method use
consensus method for prediction in general and is the combined form of three
different methods (ANN, SMM and combinatorial library).

6- I selected IEDB prediction method and MHC source specie
was human. Allele name and length was HLA-A*2:06 and 14 respectively.

7- In the end, I choose the output
format that was XHTML table.

·        
Results:

When I submitted, the whole protein
sequence is divided into short peptide sequence of specific length that I
choose. The affinity of short peptide is calculated in the tabular form.  The results in the table showed binding
affinity and ability of epitope to a specific MHC-1 molecule and to wat extent
the binding will occur. It comes to know that the less the percentile rank, the
more or strong binding will occur between MHC-1 and epitope of antigen.

·        
Function:

 IMMUNE EPITOPE DATABASE AND ANALYSIS
RESOURCE (IEDB) was developed to help biomedical researchers to improved
vacations processes. It also helps researchers to develop diagnostics and
therapeutics techniques. This method functions in providing a epitope analysis
variety and prediction tools. The IEDB covers a huge amount of epitope data
which is experimentally defined or derived. This method is also linked with
other resources and tools as well.