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Benchmark datasets of immune receptor-epitope structural complexes.

Swapnil Mahajan1, Zhen Yan2, Martin Closter Jespersen3

  • 1Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA. swapnil@lji.org.

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|October 12, 2019
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Summary

A new webserver, SCEptRe, provides weekly updated, customizable datasets of immune receptor-epitope structural complexes. These resources are essential for developing and validating advanced epitope prediction tools for diagnostics and therapeutics.

Keywords:
AntibodyEpitopeEpitope predictionIEDBMHCProtein structuresTCR

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Area of Science:

  • Immunology
  • Structural Biology
  • Bioinformatics

Background:

  • Accurate epitope prediction is crucial for disease diagnostics, treatment, and vaccine development.
  • Emerging methods leverage antibody and T-cell receptor (TCR) sequence data for receptor-specific epitope prediction.
  • High-quality, up-to-date receptor-antigen complex datasets are needed to validate these advanced prediction tools.

Purpose of the Study:

  • To create a resource for generating benchmark datasets for receptor-specific epitope prediction tools.
  • To address the need for regularly updated, high-quality structural complex data.

Main Methods:

  • Developed the SCEptRe (Structural Complexes of Epitope-Receptor) webserver.
  • SCEptRe weekly extracts and clusters 3D antibody-antigen, TCR-pMHC, and MHC-ligand complexes from the Immune Epitope Database.
  • Provides annotated receptor information (e.g., CDR sequences, VDJ genes) and allows user customization of datasets based on structural quality and clustering parameters.

Main Results:

  • SCEptRe generates comprehensive, weekly updated benchmark datasets of immune receptor-epitope structural complexes.
  • The datasets are clustered based on antigen, receptor, and epitope features.
  • Users can tailor datasets by setting thresholds for resolution, R-free factor, and sequence identity.

Conclusions:

  • SCEptRe offers valuable, user-customized datasets for the development and benchmarking of epitope prediction tools.
  • These resources will aid in advancing receptor-specific epitope prediction methodologies.
  • The SCEptRe webserver is freely accessible for research use.