Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
Methods Mol Biol. 2023;2552:283-294. doi: 10.1007/978-1-0716-2609-2_15.
Antibody and TCR modeling are becoming important as more and more sequence data becomes available to the public. One of the pressing questions now is how to use such data to understand adaptive immune responses to disease. Infectious disease is of particular interest because the antigens driving such responses are often known to some extent. Here, we describe tips for gathering data and cleaning it for use in downstream analysis. We present a method for high-throughput structural modeling of antibodies or TCRs using Repertoire Builder and its extensions. AbAdapt is an extension of Repertoire Builder for antibody-antigen docking from antibody and antigen sequences. ImmuneScape is a corresponding extension for TCR-pMHC 3D modeling. Together, these pipelines can help researchers to understand immune responses to infection from a structural point of view.
抗体和 TCR 建模正变得越来越重要，因为越来越多的序列数据可供公众使用。现在一个紧迫的问题是如何利用这些数据来了解对疾病的适应性免疫反应。传染病尤其令人关注，因为驱动这种反应的抗原在某种程度上通常是已知的。在这里，我们描述了收集数据并对其进行清理以用于下游分析的技巧。我们提出了一种使用 Repertoire Builder 及其扩展进行抗体或 TCR 高通量结构建模的方法。AbAdapt 是 Repertoire Builder 的一个扩展，用于从抗体和抗原序列进行抗体-抗原对接。ImmuneScape 是 TCR-pMHC 3D 建模的对应扩展。这些管道一起可以帮助研究人员从结构角度了解对感染的免疫反应。
