Table of contents

1. How to utilize the Pep2TCR website for predictions

   • Notices

   • Single Mode

   • Batch Mode

2. How to search the collected database

3. Additional Resources

How to utilize the Pep2TCR website for predictions

Pep2TCR offers two modes: Single mode and Batch mode. Below is the help messages for Pep2TCR:

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usage: Pep2TCR.py [-h] [--mode {single,batch}] [--cdr3 CDR3] [--pep PEP] [--data_path DATA_PATH] [--outdir OUTDIR]
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optional arguments:
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  -h, --help            show this help message and exit
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  --mode {single,batch} default is single mode
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  --cdr3 CDR3
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  --pep PEP
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  --data_path DATA_PATH csv format, first column is CDR3, second column is Epitope
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  --outdir OUTDIR       default is . (current directory)

Single Mode

Users can input a single CDR3-peptide pair to predict binding probability. For the correct input format of CDR3 and Peptide, please refer to the Notice section.

Batch Mode

For users who have a substantial number of CDR3-peptide pairs to predict, we also offer a Batch Mode. Users simply need to click the "Browse" button, upload the CSV file in the following format:

If some of the pairs in the uploaded file do not meet the requirements outlined in the Notice, the predictive results for those pairs will be empty.

Notices

• Restrict the length of CD4 TCRβ's CDR3 region to 8-20 and the Epitope's length to 9-20.

• Please use only the 20 common amino acids as inputs. Avoid including anomalous amino acids and unrelated special characters.

• We suggest utilizing a prediction score of 0.5, a rank of 0.05 for strong binding and 0.10 for weak binding, users can adjust them based on individual circumstances.

How to search the collected database

The Search page includes the collected CD4 dataset utilized in the Pep2TCR project, comprising a total of 4821 positive samples. Users can enter either a CDR3β sequence or a peptide, along with a specified maximum edit distance (Levenshtein distance). Subsequently, the website will identify analogous sequences within our collected CD4 dataset after clicking "Search" button.

Additional Resources

TCR-peptide interaction prediction websites:

• DLpTCR - DLpTCR Server (jianglab.org.cn)

• ERGO-I - Home Page (biu.ac.il) / ERGO-II - ERGO-II (biu.ac.il)

TCR related databases:

• TCR3d - TCR Database (umd.edu)

• IEDB - IEDB.org: Free epitope database and prediction resource

• VDJdb - VDJdb (cdr3.net)

• McPAS-TCR - Pathology-associated TCR database (weizmann.ac.il)

• TCRdb - TCRdb (hust.edu.cn)

• PIRD - PIRD: Pan immune repertoire database - CNGBdb

• dbPepNeo2.0 - http://www.biostatistics.online/dbPepNeo2