MMBPred Help Document


Introduction to server

The sever will predict promiscuous MHC class-1 binders having mutation at one, two or three position's in each predicted peptide.The promiscuous MHC binders can bind to several HLA alleles. These peptides are most suitable for subunit vaccine development because with single epitope, the immune response can be generated in large population.The mutation in the peptide may increase its binding spectrum of peptide frame.The prediction of the promiscuous MHC binding peptide is crucial due to so much MHC polymorphism. The prediction of the promiscuous MHC binding peptide will increase effectivness of vaccine in different genetic groups.The server will predict mutated binders for 46 MHC class-1 alleles.

What is the need for mutated MHC binders Prediction??

It is observed in literature that natural proteins are not always good candidate for optimal or subunit vaccine designing. The mutation of single or more amino acid may alter the immunogenic properties of the peptides. The mutation or modification in peptide can have three effects
i) The immunogenicity of peptides can be increased.This mostly occurs due to increase in binding affinity of peptide toward MHC.
ii) The peptide will bind with more number of MHC variants.
iii) The peptide may lose its immunogenic properties.

The server will predict first and second type of peptides.


Prediction Algorithm

This server utilizes matrix data in a linear prediction model, in which peptide conformation is entirely neglected. The only parameters describing peptide binding are peptide frames,effect of peptide side chain on binding and peptide length.The complete detail of algorithm can be obtained from MMBPred Algorithm page.



Instructions for prediction

Step I:

Type the following URL address in your web browser
                http://webs.iiitd.edu.in/raghava/mmbpred 

Step II: Select one of the following to display the page having prediction form.

  • Single mutated MHC binders
    This tool will predict the peptides having single positional (user defined) or random mutation.
  • Double mutated MHC binders
    This tool will predict the peptides having two positional(user defined) or random mutations.
  • Triple mutated MHC binders
    This tool will predict the peptides with three mutations at three user defined positions.
  • Epitope Enhancement

    This tool will predict the more immunogenic peptides based on the fact that high affinity binders are more immunogenic. The amino acids of the native peptide frame are replaced by the amino acid which best fit at specific position.The change of amino acid is performed at user defind position.



    • This type of page will appear


    Select all the fields, which are circled in the picture shown above. If any field left blank or not selected the server ewill not be able to run prediction.

    Step III
    1. Select one or more MHC alleles from this field.The selection of "All" from this field will run prediction for all 46 MHC alleles.The user should use ALT or Meta key for multiple selection.

    2. Paste your antigen or peptide sequence only as single letter amino acid code in provided text area .All the non-standard characters are ignored from input sequence.The processing time of server will depend upon the length of input sequence and type of mutation.The server is very efficient for modification of antigenic sequence smaller in size. 


    3. Select positional or random mutation from this field.The server can predict single or double mutated peptides having positional and random mutation.The prediction of random mutation is done by extracting peptides having all the possible sites mutated,whereas in case of positional mutation only the specified sites are mutated.For eaxmple, if user selects 2 and 9 position for mutation, then all the predicted binders have both of these sites mutated.

    4. This selection of site or position for mutation in each nonamer peptide is optional field.The value of this field is only significant for positional mutation.The value is totally neglected in case of random mutagenesis.

      • In case of single mutated MHC binder prediction, the value of position can vary from 1-9 for positional mutation.

      • In case of double mutated MHC binder prediction, the value of positions can vary from 1-9 for positional mutation.The value of both the position for mutation should be different.

      • The prediction of triple mutated peptides require three positional values.The value of three positions should be different.The random mutation is not possible in this case.The prediction of triple mutated peptide frames from long antigenic protein will take longer time.



        • The epitope enhancement is another way to predict muated MHC binders with high affinity.The user can select the positions that should not be changed. All the positions which are not selected they are mutated with the amino acid which is best fit at that site.The mutated peptide with maximum score for specific MHC allele is predicted when all the positions in peptide are mutated.


    5. The threshold is an important parameter, which is defined as the 'percentage of best scoring peptides'. For example, a threshold of 1% would predict peptides in any given protein sequence, which belong to the 1% best scoring peptides. 
      • The % threshold parameter allows the user to select for different stringency levels, in order to modulate the prediction results: a lower threshold corresponds to a high stringency prediction, i.e. to a lower rate of false positives and to a higher rate of false negatives. In contrast, a higher threshold value (low stringency) corresponds to a higher rate of false positives and a lower rate of false negatives. In short, from the same protein sequence input, a threshold setting of 1% will predict a lower number of peptide sequences and for a lower number of HLA-II alleles, compared to 2% or higher thresholds; however, this will also ensure a higher likelihood of positive downstream experimental results. Normally, at least for a first round of screening, threshold values higher than 3% are not desirable, since the rate of false positives can increase the size of the predicted repertoire to an amount unacceptable for later experimental testing.


    6. The value of this field is useful for the prediction of the promiscuous MHC binding peptides.Value in this field represent the minimum number of MHC alleles with which a peptide should bind.This is used as cut-off for the sorting of promiscuous MHC binders from predicted result.For example, if this field have value "10" then all the peptides which are predicted binder for more than or equalto 10 MHC alleles will be displayed in result.


    7. Finally click on submit button.

    Step II: Tabular Result display:

    The server will display the results in tabular form.The result will show the peptide binding with maximum number of MHC allele at Top.The results for the above query are as follows.


    Length of input sequence9
    Date of sequence scanningFri May 24 17:33:11 2002
    Threshold setting4%
    Number of alleles46
    Peptide binding with at least10  MHC allele
    Position for Mutation[in each Nonamer]2