Predicting reverse-bound peptide conformations in MHC Class II with PANDORA.

ABSTRACT: Recent discoveries have transformed our understanding of peptide binding in Major Histocompatibility Complex (MHC) molecules, showing that peptides, for some MHC class II alleles, can bind in a reverse orientation (C-terminus to N-terminus) and can still effectively activate CD4+ T cells. These finding challenges established concepts of immune recognition and suggests new pathways for therapeutic intervention, such as vaccine design. We present an updated version of PANDORA, which, to the best of our knowledge, is the first tool capable of modeling reversed-bound peptides. Modeling these peptides presents a unique challenge due to the limited structural data available for these orientations in existing databases. PANDORA has overcome this challenge through integrative modeling using algori

SUBMITTER: Rademaker DT 

PROVIDER: S-EPMC11973093 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature