CLBTope: Prediction of Linear & Conformational B-cell Epitopes

In the past number of methods have been developed either for predicting linear or conformational epitopes. First time, we had made an attempt to predict linear/continious and conformational B-cell epitopes in a protein from its sequence.
Reference: Kumar N., Tripathi S., Sharma N., Patiyal S., Devi N.L. and Raghava G.P.S. (2024)A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence. Computers in Biology and Medicine, 108083, doi.org/10.1016/j.compbiomed.2024.108083.

Module Description
The Predict module allows users to predict the B-cell epitope in a set of peptides or peptide library (virtual screening). User may submit large number of peptides and server will predict and rank them based on their potential as B-cell epitopes or non B-cell epitope.
The Design module generate mutant of a query peptide and predict B-cell epitopes in mutants. This server allows users to identify minimum mutations required to increase its potency.
The Protein scan module allows user to identify B-cell epitopes regions in a protein, which may be further removed or altered. The other way round, here users can also search a protein sequence to find out novel B-cell epitopes.

Prediction

This tool has been developed to predict B-Cell epitopes, where users are allowed to paste or upload file with multiple peptide sequences and each sequence would be the predicted according to the model selected. For more help please visit

Job/Sequence Name: [optional]:    

Enter email address[optional]:  
(Enter email if you want to receive your result via email)

Type or paste peptide sequence(s) in single letter code (in FASTA format):

    


OR   Submit sequence file:

Select Prediction Method


DPC based
Hybrid (DPC + BLAST)
Choose Probability Threshold For Hybrid method:  
Physicochemical Properties to Be Displayed :

 Amphipathicity     Charge     Hydropathicity     Hydrophilicity   

 Hydrophobicity     Molecular weight     Net Hydrogen     pI     Side bulk   
 Steric hinderance  


Designing Peptides

This module is developed for generating all possible mutant of a peptide by mutating single residue at a time. This module also predict whether mutants is B-cell or non B-cell. In summary this module allows to identify best mutant that have highest potency of being B-cell or non B-cell epitope. Server allow user to sort mutants based on their score ( probability of B-cell epitope) so user can select best mutant. In addition it allows user to further generate all possible mutants of a mutants. In summary, this module allow user to design best B-cell epitopes by identifying most important mutation in users peptide. For more help please visit .

Job/Sequence Name: [optional]:    

Enter email address[optional]:  
(Enter email if you want to receive your result via email)
Type or paste peptide sequence(s) in single letter code (in FASTA format):

    


OR   Submit sequence file:

Select Prediction Method


DPC based
Hybrid (DPC + BLAST)
Choose Probability Threshold For Hybrid method:  
Physicochemical Properties to Be Displayed :

  Amphipathicity      Hydropathicity      Hydrophilicity      Charge      Hydrophobicity   

  Molecular weight      Net Hydrogen      pI      Side bulk   

  Steric hinderance   

Protein Scan

With the help of "Protein Scan" module, the user can recognize the important regions in the protein sequence, linear or conformational epitopes. These linear or conformational epitopes causing regions may be removed or altered. Additionally, users can also identify novel linear or conformational epitopes in the given protein sequence. Further, the user can select the length of the peptide sequences fragment to predict linear or conformational epitopes. Please visit page, for more help.

Job/Sequence Name: [optional]:    

Enter email address[optional]:  
(Enter email if you want to receive your result via email)
Type or paste peptide sequence(s) in single letter code (in FASTA format):

    


OR   Submit sequence file:

Select Prediction Method


DPC based
Hybrid (DPC + BLAST)
Choose Probability Threshold For Hybrid method:  
Choose peptide fragment length:
Select Visualization approach: Graphical   Tabular  

Motif Scan

This module allows user to scan or map the B-cell epitope motifs in the query sequence. MERCI was used to derive the motifs from experimentally validated B-cell epitopes. Here, the user can search for the crucial motifs present in the query protein sequence to find out its role as a B-cell epitope or non-Bcell epitope. This module allow the users to submit the multiple protein sequences at a time in FASTA format. For more help please visit .

Job/Sequence Name: [optional]:    

Enter email address[optional]:  
(Enter email if you want to receive your result via email)
Type or paste peptide sequence(s) in single letter code (in FASTA format):

    


OR   Submit sequence file:

Physicochemical Properties to Be Displayed :

  Amphipathicity      Charge      Hydropathicity      Hydrophilicity      Hydrophobicity   

  Molecular weight      Net Hydrogen      pI   

Blast Scan

This page allows users to search the query protein sequence against the database of known linear or conformational epitopes using similarity-based search method, i.e. BLAST. This module will predict the given query sequence as a B-cell epitope either it is linear or conformational if it gets any hit from the database and non B-cell epitope if it does not get any hit from the database. It allows the users to submit the multiple protein sequences at a time in FASTA format. Please visit page, for more help.

Job/Sequence Name: [optional]:    

Enter email address[optional]:  
(Enter email if you want to receive your result via email)
Type or paste peptide sequence(s) in single letter code (in FASTA format):

    


OR   Submit sequence file:

Physicochemical Properties to Be Displayed :

  Amphipathicity      Charge      Hydropathicity      Hydrophilicity      Hydrophobicity   

  Molecular weight      Net Hydrogen      pI   


Choose E-value:

Contact Us

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Dr. Gajendra P. S. Raghava

Professor & Head Department of Computational Biology
Indraprastha Institute of Information Technology Okhla Phase 3, New Delhi, India
Email: raghava@iiitd.ac.in, raghavagps@gmail.com, raghavagps@yahoo.com

Raghava's Group Indraprastha Institute of Information Technology, Delhi