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Methods for sequence and structural analysis of B and T cell receptor repertoires

B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important rol...

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Autores principales: Teraguchi, Shunsuke, Saputri, Dianita S., Llamas-Covarrubias, Mara Anais, Davila, Ana, Diez, Diego, Nazlica, Sedat Aybars, Rozewicki, John, Ismanto, Hendra S., Wilamowski, Jan, Xie, Jiaqi, Xu, Zichang, Loza-Lopez, Martin de Jesus, van Eerden, Floris J., Li, Songling, Standley, Daron M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366105/
https://www.ncbi.nlm.nih.gov/pubmed/32802272
http://dx.doi.org/10.1016/j.csbj.2020.07.008
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author Teraguchi, Shunsuke
Saputri, Dianita S.
Llamas-Covarrubias, Mara Anais
Davila, Ana
Diez, Diego
Nazlica, Sedat Aybars
Rozewicki, John
Ismanto, Hendra S.
Wilamowski, Jan
Xie, Jiaqi
Xu, Zichang
Loza-Lopez, Martin de Jesus
van Eerden, Floris J.
Li, Songling
Standley, Daron M.
author_facet Teraguchi, Shunsuke
Saputri, Dianita S.
Llamas-Covarrubias, Mara Anais
Davila, Ana
Diez, Diego
Nazlica, Sedat Aybars
Rozewicki, John
Ismanto, Hendra S.
Wilamowski, Jan
Xie, Jiaqi
Xu, Zichang
Loza-Lopez, Martin de Jesus
van Eerden, Floris J.
Li, Songling
Standley, Daron M.
author_sort Teraguchi, Shunsuke
collection PubMed
description B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
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spelling pubmed-73661052020-07-17 Methods for sequence and structural analysis of B and T cell receptor repertoires Teraguchi, Shunsuke Saputri, Dianita S. Llamas-Covarrubias, Mara Anais Davila, Ana Diez, Diego Nazlica, Sedat Aybars Rozewicki, John Ismanto, Hendra S. Wilamowski, Jan Xie, Jiaqi Xu, Zichang Loza-Lopez, Martin de Jesus van Eerden, Floris J. Li, Songling Standley, Daron M. Comput Struct Biotechnol J Review Article B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context. Research Network of Computational and Structural Biotechnology 2020-07-17 /pmc/articles/PMC7366105/ /pubmed/32802272 http://dx.doi.org/10.1016/j.csbj.2020.07.008 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Review Article
Teraguchi, Shunsuke
Saputri, Dianita S.
Llamas-Covarrubias, Mara Anais
Davila, Ana
Diez, Diego
Nazlica, Sedat Aybars
Rozewicki, John
Ismanto, Hendra S.
Wilamowski, Jan
Xie, Jiaqi
Xu, Zichang
Loza-Lopez, Martin de Jesus
van Eerden, Floris J.
Li, Songling
Standley, Daron M.
Methods for sequence and structural analysis of B and T cell receptor repertoires
title Methods for sequence and structural analysis of B and T cell receptor repertoires
title_full Methods for sequence and structural analysis of B and T cell receptor repertoires
title_fullStr Methods for sequence and structural analysis of B and T cell receptor repertoires
title_full_unstemmed Methods for sequence and structural analysis of B and T cell receptor repertoires
title_short Methods for sequence and structural analysis of B and T cell receptor repertoires
title_sort methods for sequence and structural analysis of b and t cell receptor repertoires
topic Review Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366105/
https://www.ncbi.nlm.nih.gov/pubmed/32802272
http://dx.doi.org/10.1016/j.csbj.2020.07.008
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