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

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Table of Contents

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:

  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

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 [email protected].

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

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