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Structural Modeling of Lymphocyte Receptors and Their Antigens

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In Vitro Differentiation of T-Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2048))

Abstract

Structural modeling plays a key role in protein function prediction on a genome-wide scale. For B and T lymphocyte receptors, the critical functional question is: which antigens and epitopes are targeted? With emerging B cell receptor (BCR) and T cell receptor (TCR) sequencing methods improving in both breadth and depth, there is a growing need for methods that can help answer this question. Since lymphocyte-antigen recognition depends on complementarity, structural modeling is likely to play an important role in understanding antigen specificity and affinity. In the case of BCRs, such modeling methods have a long history in the study and design of antibodies. However, for TCRs there are relatively few publicly available modeling tools, and, to our knowledge, none that incorporate interaction between TCRs and peptide-MHC (pMHC) complexes. Here, we provide a web-based tool, ImmuneScape (https://sysimm.org/immune-scape/), to carry out TCR-pMHC modeling as a first step toward structure-based function prediction.

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Author information

Authors and Affiliations

  1. Research Institute for Microbial Diseases, Osaka University, Osaka, Japan

    Songling Li, Jan Wilamowski, Shunsuke Teraguchi, Floris J. van Eerden, John Rozewicki, Kazutaka Katoh & Daron M. Standley

  2. Immunology Frontier Research Center, Osaka University, Osaka, Japan

    Shunsuke Teraguchi, John Rozewicki, Kazutaka Katoh & Daron M. Standley

  3. Graduate School of Medicine, Osaka University, Osaka, Japan

    Ana Davila & Zichang Xu

Authors
  1. Songling Li
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  2. Jan Wilamowski
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  3. Shunsuke Teraguchi
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  4. Floris J. van Eerden
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  5. John Rozewicki
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  6. Ana Davila
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  7. Zichang Xu
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  8. Kazutaka Katoh
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  9. Daron M. Standley
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Corresponding author

Correspondence to Daron M. Standley .

Editor information

Editors and Affiliations

  1. Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan

    Shin Kaneko

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Li, S. et al. (2019). Structural Modeling of Lymphocyte Receptors and Their Antigens. In: Kaneko, S. (eds) In Vitro Differentiation of T-Cells. Methods in Molecular Biology, vol 2048. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9728-2_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9728-2_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9727-5

  • Online ISBN: 978-1-4939-9728-2

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