ahmedaq / HCV-E2

Software for in silico identification of immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them

Table of Contents

• Overview
• Details
• Requirements
• Usage
• Troubleshooting

Overview

This software package comprises scripts that include the main functions for reproducing the results presented in the paper titled "Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them".

Details

Title of paper

Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them

Authors

Ahmed A. Quadeer, Raymond H. Y. Louie, and Matthew R. McKay

Requirements

1. A PC with MATLAB (preferrably v2016b or later) installed on it with the following additional toolboxes:

   • Bioinformatics Toolbox
   • Communications System Toolbox
   • Statistics and Machine Learning Toolbox
   • Curve Fitting Toolbox
   • Parallel Computing Toolbox
   • MATLAB Distributed Computing Server
   • MATLAB supported compiler installed for compiling C files  

2. For inferring maximum-entropy model parameters:

   • Minimum probability flow method (MPF-BML), available at https://github.com/raymondlouie/MPF-BML

3. For computing the mean escape time metric using the available code, extensive computations are required. The reported escape times in the manuscript were computed using ~1 million core-hours on a supercomputer with Intel(R) Xeon(R) CPU E5-2692 v2 @ 2.20GHz.  

4. For mapping fitness costs on the available E2 crystal structure

   • Pymol, available at https://pymol.org/

Usage

1. Open MATLAB
2. Run the script main.m
3. By default, all data files are provided to reproduce the results in the paper

For visualizing the step-by-step procedure and the corresponding output

1. Download the html folder
2. Open the main.html file in your browser

Troubleshooting

For any questions or comments, please email at [e-mail].