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
Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan.
Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan.
Comput Struct Biotechnol J. 2020 Jul 17;18:2000-2011. doi: 10.1016/j.csbj.2020.07.008. eCollection 2020.
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.
B细胞受体（BCR）和T细胞受体（TCR）构成了一个重要的防御分子网络，它们共同作用能够区分自我与非自我，并促进对诸如病原体或肿瘤等携带抗原细胞的破坏。BCR和TCR库的分析在基础免疫学以及生物技术中都发挥着重要作用。由于这些库具有高度多样性，因此需要专门的软件方法从BCR和TCR序列数据中提取有意义的信息。在此，我们综述了用于分析BCR和TCR库的生物信息学工具的最新进展，重点关注那些纳入结构特征的工具。在描述了免疫受体库的最新测序技术之后，我们调查了BCR和TCR的结构建模方法以及对这些模型进行聚类的方法。我们综述了下游分析，包括BCR和TCR表位预测、抗体-抗原对接以及TCR-肽-MHC建模。我们还在此背景下简要讨论了分子动力学。
