Epitope Prediction Calculator

About the Epitope Prediction Calculator

The Epitope Prediction Calculator is a free, scientifically accurate online tool that predicts linear B-cell epitopes and MHC class I T-cell epitopes from any protein sequence using peer-reviewed algorithms. Whether you are working on vaccine design, immunotherapy, diagnostic development, or basic immunology research, this epitope prediction calculator delivers reliable results instantly.

Epitopes are the specific parts of an antigen recognized by the immune system — specifically by antibodies, B cells, or T cells. Accurate epitope prediction is crucial in modern biotechnology and has direct applications in peptide vaccine development, cancer immunotherapy (neoantigen prediction), allergy research, and infectious disease studies.

Scientific Foundation of This Calculator

This tool combines two gold-standard, peer-reviewed methods:

• B-cell epitope prediction: BepiPred-2.0 (Jespersen et al., 2017, Journal of Immunology) – Random Forest algorithm trained on antibody-antigen crystal structures (threshold ≥ 0.5 recommended for high specificity).
• T-cell (MHC-I) epitope prediction: Based on NetMHCpan-4.1 binding affinity matrix (Reynisson et al., 2020, Nucleic Acids Research). Peptides with IC50 < 500 nM are considered strong binders.

Why Use an Epitope Prediction Calculator?

Traditional experimental epitope mapping (e.g., peptide arrays, ELISA, X-ray crystallography) is expensive and time-consuming. Computational epitope prediction reduces the search space from thousands to a handful of high-probability candidates, saving months of lab work and millions in costs. Leading COVID-19, cancer, and malaria vaccines used epitope prediction in their design pipeline.

When Should You Use This Tool?

• Designing subunit or peptide vaccines
• Identifying neoantigens in cancer immunotherapy
• Studying antibody responses in infectious diseases
• Developing therapeutic monoclonal antibodies
• Academic research in immunology and structural biology

How to Use the Epitope Prediction Calculator (User Guidelines)

1. Paste your protein sequence (FASTA or plain text, single-letter code only).
2. Choose the desired MHC allele (HLA-A*02:01 covers ~50% of the global population).
3. Select peptide length (9-mer is standard for MHC-I).
4. Click “Calculate Epitopes”.
5. Review B-cell scores (higher = more likely to be epitope) and T-cell binding affinity (IC50 < 500 nM = strong binder).

Interpretation of Results

B-cell Epitopes: Residues with BepiPred-2.0 score ≥ 0.55 are highlighted in green and considered highly likely linear B-cell epitopes.

T-cell Epitopes: Top 10 predicted peptides are ranked by predicted binding affinity (lower IC50 = stronger binding). Percentile rank < 2% indicates strong binder.

Limitations & Best Practices

Linear epitope prediction works best for continuous epitopes. Conformational (discontinuous) epitopes require 3D structure-based tools. Always validate top predictions experimentally (e.g., ELISA, T-cell activation assays).

For more in-depth information about epitopes, visit the Wikipedia page on Epitope Prediction.

This tool is proudly powered by open-science principles and brought to you by Agri Care Hub – your trusted resource for bioinformatics and agricultural biotechnology tools.

References

• Jespersen MC, et al. (2017). BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res.
• Reynisson B, et al. (2020). NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation. Nucleic Acids Res.
• Vita R, et al. (2019). The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res.

Last updated: December 2025. This Epitope Prediction Calculator is free for academic and commercial use with no registration required.