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Bioinformatics Programming

vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

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vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obtained from Autodock Vina. In this article, we have provided another script to search for binding affinity associated with a compound.

Users can easily search for specific binding affinities by providing a compound name given that the same name is present in the log filename.

Usage

Download the file from our GitHub account and save it in the directory where you have kept all log files. If you will save it elsewhere, don’t forget to provide the full path to this file. It will run on Linux as well as on Windows.

Run it using Python 3.x.

$ python3 vs_analysis_compound.py <compound-name>

OR if Python 3.x is in your path then just type the following:

$ python vs_analysis.py <compound-name>

Example

For example, if you have hundreds of log files and one is named log_naphthalene.txt, then you can provide naphthalene as a compound name. The script will display its binding affinity. You can run it as shown below:

$ python3 vs_analysis_compound.py naphthalene

Availability

The script is freely available to download from our GitHub account.


NOTE:

  • This script screens for the log files containing the word ‘log’ in their filenames, e.g., “log_compound1.txt” or “log_methanol.txt”
  • It is required to name your log files along with the name of a compound.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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