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CDpred: Prediction of celiac disease associated epitopes and motifs in a protein

CDpred is a comprehensive, manually curated database and analysis platform dedicated to the identification and study of epitopes and motifs associated with celiac disease. This resource consolidates experimental data on peptides that trigger an immune response in celiac disease patients, providing a critical tool for researchers working on diagnostics, therapeutics, and safe food product development.

Dataset -> cdpred

Model & Scripts -> cdpred-main

Web Server: https://webs.iiitd.edu.in/raghava/cdpred/index.php

Citation

Tomer R, Patiyal S, Dhall A and Raghava GPS (2023) Prediction of celiac disease associated epitopes and motifs in a protein. Front. Immunol. 14:1056101. doi: 10.3389/fimmu.2023.1056101

This dataset can also be found on Zenodo at https://doi.org/10.5281/zenodo.20082119

About the Research

Celiac disease is a chronic autoimmune disorder triggered by the ingestion of gluten proteins found in wheat, barley, and rye. The identification of specific immunogenic sequences (epitopes) and patterns (motifs) within these proteins is essential for understanding the molecular basis of the disease and for the safety assessment of proteins in various food products.

  • Data Compilation: The database contains 704 experimentally validated celiac disease-associated epitopes manually curated from a vast amount of published literature.

  • Motif Identification: Systematic analysis was conducted to identify recurring motifs, resulting in a collection of unique motifs.

Note

  • Please convert all the cdpred folder ".fasta" files in ".rtf" format.

Key Features

1. Robust Dataset

  • Celiac Disease Epitopes: A collection of experimentally validated sequences known to activate the mucosal immune response.

  • Identified Motifs: Statistically significant patterns derived from the epitope dataset to help predict the immunogenicity of new sequences.

  • Diverse Source Proteins: Data includes sequences from various gluten-forming proteins like gliadins, glutenins, hordeins, and secalins.

2. Predictive and Analysis Tools

CDpred offers several modules to assist the scientific community in analyzing protein sequences for celiac toxicity:

  • Epitope Mapping: Allows users to map known celiac-associated epitopes onto a query protein sequence.

  • Motif Scanning: Users can scan their sequences for the presence of the identified celiac motifs.

  • Similarity Search: Integrated BLAST tool to find similarities between query sequences and the database of validated epitopes.

3. Integrated Web-Bench

  • Browse & Search: Effortlessly explore epitopes based on their source organism, protein type, or specific motifs.

  • Protein Analysis: A dedicated module for predicting the potential "celiac-safe" or "celiac-toxic" nature of a protein.

Applications

  • Food Safety: Screening novel or genetically modified crops for potential celiac-triggering sequences.

  • Therapeutic Development: Assisting in the design of peptide-based vaccines or enzyme therapies intended to degrade immunogenic gluten peptides.

  • Diagnostic Research: Identifying high-potency epitopes for use in T-cell-based diagnostic assays or blood tests.

Contact & Authors

Prof. Gajendra P. S. Raghava (Corresponding Author)

raghava@iiitd.ac.in

Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT Delhi), New Delhi, India.

Support

The development of CDpred was supported by the Department of Biotechnology (DBT) and the Council of Scientific and Industrial Research (CSIR), Government of India. Infrastructure and facilities were provided by IIIT-Delhi.