Methods for sequence and structural analysis of B and T cell receptor repertoires
Methods for sequence and structural analysis of B and T cell receptor repertoires
复制标题
DOI：
10.1016/j.csbj.2020.07.008
复制
发表时间：
2020-07
影响因子：
6
通讯作者：
Shunsuke Teraguchi;Dianita S. Saputri;M. Llamas-Covarrubias;Ana Davila;Diego Diez;Sedat Aybars Nazlica;John Rozewicki;Hendra S. Ismanto;Jan Wilamowski;Jiaqi Xie;Zichang Xu;M. Loza-Lopez;Floris J. van Eerden;Songling Li;D. Standley
中科院分区：
文献类型：
--
作者：
Shunsuke Teraguchi;Dianita S. Saputri;M. Llamas-Covarrubias;Ana Davila;Diego Diez;Sedat Aybars Nazlica;John Rozewicki;Hendra S. Ismanto;Jan Wilamowski;Jiaqi Xie;Zichang Xu;M. Loza-Lopez;Floris J. van Eerden;Songling Li;D. Standley
B细胞受体（BCR）和T细胞受体（TCR）组成了一个重要的防御分子网络，这些防御分子共同可以区分自我和非自我，并有助于破坏携带抗原的细胞，如病原体或肿瘤。BCR和TCR库的分析在基础免疫学以及生物技术中起着重要作用。因为库是高度多样化的，所以需要专门的软件方法来从BCR和TCR序列数据中提取有意义的信息。在这里，我们回顾了生物信息学工具的最新发展，用于分析BCR和TCR库，重点是那些纳入结构特征。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，沿着了聚类这些模型的方法。本文综述了BCR和TCR表位预测、抗体-抗原对接和TCR-肽-MHC建模等下游分析方法。我们也简要讨论了分子动力学在这方面。
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.