PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes.Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks.  We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here.  Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process.  On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models.  PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed.  PANDORA is a modularized and user-configurable python package with easy installation.  We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
PANDORA
PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes.Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks.  We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here.  Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process.  On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models.  PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed.  PANDORA is a modularized and user-configurable python package with easy installation.  We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
PANDORA
PANDORA is a modularized and user-configurable python package with easy installation. 
Python