Structural Modeling of Adaptive Immune Responses to Infection

Tina Lusiany; Zichang Xu; Dianita S Saputri; Hendra S Ismanto; Sedat Aybars Nazlica; Daron M Standley

doi:10.1007/978-1-0716-2609-2_15

Structural Modeling of Adaptive Immune Responses to Infection

Methods Mol Biol. 2023:2552:283-294. doi: 10.1007/978-1-0716-2609-2_15.

Authors

Tina Lusiany¹, Zichang Xu¹, Dianita S Saputri¹, Hendra S Ismanto¹, Sedat Aybars Nazlica¹, Daron M Standley²

Affiliations

¹ Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
² Research Institute for Microbial Diseases, Osaka University, Suita, Japan. standley@biken.osaka-u.ac.jp.

PMID: 36346598
DOI: 10.1007/978-1-0716-2609-2_15

Abstract

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.

Keywords: Antibody; Sequence; Structure modeling; T-cell receptor.

MeSH terms

Antigens*
Immunity
Receptors, Antigen, T-Cell*

Substances

Receptors, Antigen, T-Cell
Antigens