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    General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept

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    Author
    Antunes, Dinler A.; Devaurs, Didier; Moll, Mark; Lizée, Gregory; Kavraki, Lydia E.
    Date
    2018
    Abstract
    The class I major histocompatibility complex (MHC) is capable of binding peptides derived from intracellular proteins and displaying them at the cell surface. The recognition of these peptide-MHC (pMHC) complexes by T-cells is the cornerstone of cellular immunity, enabling the elimination of infected or tumoral cells. T-cell-based immunotherapies against cancer, which leverage this mechanism, can greatly benefit from structural analyses of pMHC complexes. Several attempts have been made to use molecular docking for such analyses, but pMHC structure remains too challenging for even state-of-the-art docking tools. To overcome these limitations, we describe the use of an incremental meta-docking approach for structural prediction of pMHC complexes. Previous methods applied in this context used specific constraints to reduce the complexity of this prediction problem, at the expense of generality. Our strategy makes no assumption and can potentially be used to predict binding modes for any pMHC complex. Our method has been tested in a re-docking experiment, reproducing the binding modes of 25 pMHC complexes whose crystal structures are available. This study is a proof of concept that incremental docking strategies can lead to general geometry prediction of pMHC complexes, with potential applications for immunotherapy against cancer or infectious diseases.
    Citation
    Antunes, Dinler A., Devaurs, Didier, Moll, Mark, et al.. "General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept." Scientific Reports, 8, (2018) Springer Nature: https://doi.org/10.1038/s41598-018-22173-4.
    Published Version
    https://doi.org/10.1038/s41598-018-22173-4
    Type
    Journal article
    Publisher
    Springer Nature
    Citable link to this page
    https://hdl.handle.net/1911/102433
    Rights
    This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. 
    Link to License
    https://creativecommons.org/licenses/by/4.0/
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    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map