DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

Magnus Haraldson Høie, Frederik Steensgaard Gade, Julie Maria Johansen, Charlotte Würtzen, Ole Winther, Morten Nielsen*, Paolo Marcatili

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

51 Downloads (Pure)

Abstract

Accurate computational identification of B-cell epitopes is crucial for the development of vaccines, therapies, and diagnostic tools. However, current structure-based prediction methods face limitations due to the dependency on experimentally solved structures. Here, we introduce DiscoTope-3.0, a markedly improved B-cell epitope prediction tool that innovatively employs inverse folding structure representations and a positive-unlabelled learning strategy, and is adapted for both solved and predicted structures. Our tool demonstrates a considerable improvement in performance over existing methods, accurately predicting linear and conformational epitopes across multiple independent datasets. Most notably, DiscoTope-3.0 maintains high predictive performance across solved, relaxed and predicted structures, alleviating the need for experimental structures and extending the general applicability of accurate B-cell epitope prediction by 3 orders of magnitude. DiscoTope-3.0 is made widely accessible on two web servers, processing over 100 structures per submission, and as a downloadable package. In addition, the servers interface with RCSB and AlphaFoldDB, facilitating large-scale prediction across over 200 million cataloged proteins. DiscoTope-3.0 is available at: https://services.healthtech.dtu.dk/service.php?DiscoTope-3.0.

Original languageEnglish
Article number1322712
JournalFrontiers in Immunology
Volume15
Number of pages12
ISSN1664-3224
DOIs
Publication statusPublished - 2024

Keywords

  • Antibody epitope prediction
  • B cell epitope prediction
  • ESM-IF1
  • Immunogenicity prediction
  • Inverse-folding
  • Structure-based
  • Vaccine design

Fingerprint

Dive into the research topics of 'DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations'. Together they form a unique fingerprint.

Cite this