This repository provides a detailed explanation for the computational design process for site 0 and site IV epitope-focused immunogens, published in Science: DOI: 10.1126/science.aay5051
We present two different design approaches to design scaffolds for RSVF antigenic site 0 (a discontinuous segment composed of a loop and a kinked alpha helix), as well as for antigenic site IV (a bulged beta strand). The first approach is based on design templates found in existing protein structures (template-based). Our second approach is a template-free, motif-centric design algorithm called TopoBuilder. Within this repository, we provide a detailed explanation of both design approaches, including all scripts for the computational design using Rosetta as well as for the data analysis.
For a more in-depth explanation of the TopoBuilder with additional examples, instructions for installation and usage, please visit our TopoBuilder GitHub repository.