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

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dc.citation.articleNumber4327en_US
dc.citation.journalTitleScientific Reportsen_US
dc.citation.volumeNumber8en_US
dc.contributor.authorAntunes, Dinler A.en_US
dc.contributor.authorDevaurs, Didieren_US
dc.contributor.authorMoll, Marken_US
dc.contributor.authorLizée, Gregoryen_US
dc.contributor.authorKavraki, Lydia E.en_US
dc.date.accessioned2018-07-16T18:43:47Zen_US
dc.date.available2018-07-16T18:43:47Zen_US
dc.date.issued2018en_US
dc.description.abstractThe 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.en_US
dc.identifier.citationAntunes, Dinler A., Devaurs, Didier, Moll, Mark, et al.. "General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept." <i>Scientific Reports,</i> 8, (2018) Springer Nature: https://doi.org/10.1038/s41598-018-22173-4.en_US
dc.identifier.doihttps://doi.org/10.1038/s41598-018-22173-4en_US
dc.identifier.urihttps://hdl.handle.net/1911/102433en_US
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.rightsThis 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. en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleGeneral Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concepten_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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