Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Structure-based antibody
and antigen design has advanced greatly
in recent years, due not only to the increasing availability of experimentally
determined structures but also to improved computational methods for
both prediction and design. Constant improvements in performance within
the Rosetta software suite for biomolecular modeling have given rise
to a greater breadth of structure prediction, including docking and
design application cases for antibody and antigen modeling. Here,
we present an overview of current protocols for antibody and antigen
modeling using Rosetta and exemplify those by detailed tutorials originally
developed for a Rosetta workshop at Vanderbilt University. These tutorials
cover antibody structure prediction, docking, and design and antigen
design strategies, including the addition of glycans in Rosetta. We
expect that these materials will allow novice users to apply Rosetta
in their own projects for modeling antibodies and antigens.

基于结构的抗体与抗原设计近年来取得了长足进展，这不仅得益于实验解析结构的可获取性持续提升，也归功于预测与设计两类计算方法的不断优化。面向生物分子建模的Rosetta软件套件在性能上的持续迭代，推动了结构预测应用场景的大幅拓展，涵盖抗体与抗原建模所需的对接及设计应用案例。本文综述了当前利用Rosetta开展抗体与抗原建模的主流实验流程，并以范德堡大学（Vanderbilt University）Rosetta工作坊原创的详细教程对上述流程进行演示。本系列教程涵盖抗体结构预测、对接与设计，以及抗原设计策略，其中包含在Rosetta中添加聚糖（glycans）的操作方法。我们期望本教程能够帮助入门用户在自身的抗体与抗原建模研究项目中应用Rosetta软件。