The PANDORA Software for Anchor-Restrained Peptide:MHC Modeling

Major histocompatibility complexes (MHCMajor histocompatibility complex (MHC)) play a key role in the immune surveillance system in all jawed vertebrates. MHC class IMHC class I (MHC I) molecules randomly sample cytosolic peptides from inside the cell, while MHC class IIMHC class II (MHC II) sample exogenous peptides. Both types of peptide:MHCMajor histocompatibility complex (MHC) complex are then presented on the cell surface for recognition by αβ T cells (CD8+ and CD4+, respectively). The three-dimensional structureStructures of such complexes can give crucial insights in the presentation and recognition mechanisms. For this reason, softwares like PANDORA have been developed to rapidly and accurately generate peptide:MHCMajor histocompatibility complex (MHC) (pMHC) 3D structuresStructures. In this chapter, we describe the protocol of PANDORA. PANDORA exploits the structural knowledge on anchor pockets that MHCMajor histocompatibility complex (MHC) molecules use to dock peptides. PANDORA provides anchor positions as restraints to guide the modeling process. This allows PANDORA to generate twenty 3D models in just about 5 min. PANDORA is highly customizable, easy to install, supports parallel processing, and is suitable to provide large datasets for deep learningDeep learning algorithmsAlgorithms.