HIV-1 Matrix Builder

Welcome to our site

This site will provide you with the tools and step-by-step guide to build HIV-1 Matrix (MA) shells using methods described by Sun W, et al. (2019) Mathematical determination of the HIV-1 matrix shell structure and its impact on the biology of HIV-1. PLOS ONE 14(11): e0224965.

Technical Overview

We will introduce you to 4 scripts, each of which will allow you to develop unique outcomes:

System Requirements

Python 3 support (Recommended)

  1. Python 3.5 or greater

  2. Anaconda3 > Jupytor NoteBook

  3. Python Env Library in Jupytor NoteBook:

  4. Basemap 1.2.0 or greater

  5. PyMol 2.3.2 or greater

  6. Pandas 0.24.2 or greater

Getting Started

Open Anaconda and create a python 3.5 environment

Install basemap, PyMol, pandas libraries

If a library(s) is not in your Anaconda package, follow the commands bellow

points-plot

conda install -c anaconda basemap 
conda install -c anaconda pandas 
conda install -c schrodinger pymol

Then open the main_flow.ipynb file.

You should run the code successfully as shown here.

Python 2.7 Support

Note: We recommend using the Anaconda environment system described under "Getting Started". The instructions under "Python 2.7 Support" do not need to be followed if you used the Anaconda environment described above.

  1. Python 2.7

  2. Python Libraries: importlib, matplotlib, mpl_toolkits

  3. PyMol 1.72 or greater

>python calculate_trimer_coordinates.py
Input the R: 
632
Do you want to use default r = 52.0769942809? (y or n): 
y

Then you will receive the following message and two output files >> 'points' and 'lines'

There are 1024 points.

There are 1024 points' coordinations in the points file and there is another file lines that provides the relationship between the center-of-mass of each trimer and their coordination.

You will be given an option to quickly view what the plots look like. You could input 3 to quit this script.

1 - show and save the lines plot
2 - show and save the points model
3 - quit

points-plot

lines-plot

Generation of PyMol Model

python pymol_plot_trimer.py

If your machine supports PyMol, then PyMol will open and run the script within pymol itself.

After the models are generated in PyMol, you may store your models in pdb or pse file formats from PyMol.

Generation of Flatten PyMol Model

> python calculate_flatten_trimmer_coordinations.py

Which will transfer points output file to points-2D

Then you run

> python pymol_2D_plot_trimer.py

After the models are generated in PyMol, you may store your models in pdb or pse file formats from PyMol.

Relationship Between HIV-1 MA Radius and Number of Trimer Units

> python tabulate_relationship_of_R_and_trimer_number.py

Then you need to input minimum (Min) Radius, maximum (Max) Radius, and size of the interval steps (interval). The default r referse to the distance between adjacent trimers. All units are in Angstroms.

E.g.:

Input the Min Radius: 600
Input the Max Radius: 700
Input the interval: 10
Do you want to use default r = 52.0769942809? (y or n): y

The script will output how many trimer units can fit in spheres for each HIV-1 MA radius.

E.g.:

909
955
971
1019
1033
1074
1124
1157
1178
1185
1243

Term of use

ACADEMIC PUBLIC LICENSE: This license contains the terms and conditions of using HIV-1 Matrix Builder in noncommercial settings: at academic institutions for teaching and research use, and at non-profit research organizations. You will find that this license provides noncommercial users of HIV-1 Matrix Builder with rights that are similar to the well-known GNU General Public License (GPL), yet it retains the possibility for HIV-1 Matrix Builder authors to financially support the development by selling commercial licenses. In fact, if you intend to use HIV-1 Matrix Builder in a "for-profit" environment, where research is conducted to develop or enhance a product, is used in a commercial service offering, or when a commercial company uses HIV-1 Matrix Builder to participate in a research project (for example government-funded or EU-funded research projects), then you need to obtain a commercial license for HIV-1 Matrix Builder. In that case, please contact the Author to inquire about commercial licenses.

What are the rights given to noncommercial users? Similarly to GPL, you have the right to use the software, to distribute copies, to receive source code, to change the software and distribute your modifications or the modified software. Also similarly to the GPL, if you distribute verbatim or modified copies of this software, they must be distributed under this license.

By modeling the GPL, this license guarantees that you're safe when using HIV-1 Matrix Builder in your work, for teaching or research. This license guarantees that HIV-1 Matrix Builder will remain available free of charge for nonprofit use. You can modify HIV-1 Matrix Builder to your purposes, and you can also share your modifications. Even in the unlikely case of the authors abandoning HIV-1 Matrix Builder entirely, this license permits anyone to continue developing it from the last release, and to create further releases under this license.

How to cite HIV-1 Matrix Builder:

Weijie Sun, Eduardo Reyes-Serratos, David Barilla, Joy Ramielle L. Santos, Mattéa Bujold, Sean Graves and Marcelo Marcet-Palacios. (2019) Mathematical determination of the HIV-1 matrix shell structure and its impact on the biology of HIV-1. PLOS ONE 14(11): e0224965.

Please contact Weijie Sun at weijie2@ualberta.ca for technical support.

Please contact Dr. Marcelo Marcet-Palacios at marcelo@ualberta.ca for commercial license inquiries.