PyVkabat

About PyVkabat

PyVkabat is a bioinformatics/computational chemistry tool used to calculated secondary structure variability at each residue position in a protein of interest. To reduce run time, each of the requests are made in parallel.

IMPORTANT NOTE:
Because this script makes requests to web servers, it is important that it is never used in parallel. This is important because, if this script were to be ran in parallel, certain webservers could become overwhelmed by the number of simultaneous requests and crash. This could lead to incomplete data being returned and causing others in the research community, who may rely on these servers, a great inconvenience.

Vkabat equation

Vkabat = k * N / n1

where:

• k is the number of secondary structure classes predicted for a residue
• N is the total number of predictions made for a given residue
• n1 is how often the most predicted secondary structure is observed for a residue

PyVkabat web servers used

PyVkabat submits the user's protein sequence of interest to 15 different algorithms:

• gor1
• gor3
• dpm
• sopm
• predator
• hnn
• dsc
• mlrc
• yaspin
• jpred
• phd
• prof
• sspro
• jnet
• psipred

Installation Guide

Prerequisite Software

• Miniconda or Annaconda
• Windows or Linux or Mac

Instructions

After downloading the repository and successfully installing the prerequisite software on your machine, navigate to the project directory. In the command prompt, enter the following:

conda create -n PyVkabat python=3.10 -y

Next, enter the following:

conda activate PyVkabat

Now, enter the following (make sure you are in the directory where pyvkabat_requirements.txt is located):

pip install -r pyvkabat_requirements.txt

If the previous command did not return any errors, you have successfully installed python and the required python packages to run the program. Now just clean up by entering the following command:

conda deactivate

That's it, you're done!

Running the program

To run the program, open the command prompt. You can navigate to the project folder by entering the following:

cd <PATH TO PROJECT FOLDER>

Now that you are in the project folder, enter the following command:

conda activate PyVkabat && python ./PyVkabat.py