Abstract
Major histocompatibility complexes (MHC) play a key role in the immune surveillance system in all jawed vertebrates. MHC class I molecules randomly sample cytosolic peptides from inside the cell, while MHC class II sample exogenous peptides. Both types of peptide:MHC complex are then presented on the cell surface for recognition by αβ T cells (CD8+ and CD4+, respectively). The three-dimensional structure 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:MHC (pMHC) 3D structures. In this chapter, we describe the protocol of PANDORA. PANDORA exploits the structural knowledge on anchor pockets that 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 learning algorithms.
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Acknowledgments
This project is supported by the Hypatia Fellowship from Radboudumc (Rv819.52706) and Open eScience grant from the Netherlands eScience Center (NLESC.OEC.2021.008). FP acknowledges a visiting scholarship from the Department of Scholarships and Students’ Affairs Abroad, Ministry of Science, Research and Technology, Iran.
The authors sincerely thank Gayatri Ramakrishnan, Max Luppes, Coos Baakman, Heleen Severin, and Nicolas Renaud for suggestions and proofreading.
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Marzella, D.F., Crocioni, G., Parizi, F.M., Xue, L.C. (2023). The PANDORA Software for Anchor-Restrained Peptide:MHC Modeling. In: Reche, P.A. (eds) Computational Vaccine Design. Methods in Molecular Biology, vol 2673. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3239-0_18
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DOI: https://doi.org/10.1007/978-1-0716-3239-0_18
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