Bioinformatics News
VS_Analysis: A Python package to perform post-virtual screening analysis
Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.
Introduction
Welcome to the VS-Analysis Python package, a powerful toolkit designed to streamline the analysis of virtual screening results. This open-source package namely, VS_Analysis is a valuable resource for researchers and scientists engaged in the field of bioinformatics.
This package allows you to:
- find the binding affinities of a selected number of docked compounds,
- sort the binding affinities based on a binding affinity cut-off value (provided by the user) of a selected number of compounds,
- find the specific binding affinity of a docked compound,
- calculate the number of polar hydrogen bonds between the protein and the docked compounds including all poses,
- calculate the distances of these hydrogen bonds, and
- list the names of amino acid residues that are present near the ligand within a specified distance (default distance is 3.2 Angstroms).
Key Features
The VS-Analysis package encompasses several Python scripts, each tailored to facilitate specific aspects of result analysis. Let’s take a brief look at the core scripts:
- vs_analysis.py:
- A versatile script offering a comprehensive analysis of virtual screening results generated by Autodock Vina.
- Provides insights into polar hydrogen bonds, distances, and other crucial parameters.
- Simplifies the analysis process, particularly for large datasets.
- vs_analysis_compounds.py:
- Specialized script focusing on the analysis of compounds within the virtual screening results.
- Extracts and presents detailed information about individual compounds, aiding in the identification of promising candidates.
- vs_interaction_analysis.py
- precise insights into the dynamics between ligands and target molecules.
- calculates the polar hydrogen bonds and their distances between the protein and the docked ligand.
- lists all amino acids that lie in the ligand affinity within a specified distance.
Usage
The VS_Analysis package comprises Python scripts that are straightforward to execute. Please note to exclusively use Python 3; otherwise, these scripts may encounter errors. The results will be provided in separate output files.
Availability
The VS_Analysis package is freely accessible on 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.
How to cite:
Faiza, M., 2024. VS_Analysis: A Python package to perform post-virtual screening analysis, 10(1): page 8-12. https://bioinformaticsreview.com/20240110/vs_analysis-a-python-package-to-perform-post-virtual-screening-analysis/
Bioinformatics News
Proteins shape analyses reveal novel forms and connections.
A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].
Bioinformatics News
What is MANE project?
MANE is a collaborative project between NCBI and EMBL-EBI. It stands for Matched Annotation from NCBI and EMBL-EBI [1]. The datasets provided by NCBI and EMBL-EBI on the human genome are not identical across every gene.
Bioinformatics News
This Month in Bioinformatics- Research Updates of March 2022
Here are the latest research developments in the field of bioinformatics made in the month of March 2022. (more…)
Bioinformatics News
This month in Bioinformatics- Research Updates of November 2021
We summarize the latest research published this month in the field of bioinformatics. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of October 2021
In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)
Bioinformatics News
BLAST+ 2.12.0- A more efficient version of BLAST is available
A new more efficient version of BLAST+ 2.12.o is available now [1]. This version provides more efficient multithreaded searches. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of June 2021
In this article, we summarize the latest interesting findings made this month of June in bioinformatics. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of May 2021
In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)
Bioinformatics Research Updates
This Month in Bioinformatics- Research Updates of April 2021
In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of March 2021
Here, we summarize the latest interesting findings made this month in bioinformatics. (more…)
Bioinformatics Research Updates
This Month in Bioinformatics- Research Updates of February 2021
We summarize the research done in bioinformatics in the month of February. (more…)
Bioinformatics Research Updates
This Month in Bioinformatics- Research Updates of January 2021
In this article, we summarize the main findings made in bioinformatics this month. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of December 2020
In this article, we summarize the latest research in bioinformatics published this month. (more…)
Bioinformatics News
Join Bioinformatics Review Research Group
We are going to lead a few bioinformatics research projects. For that, we are creating a new research group of Bioinformatics Review. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of November 2020
In this article, we summarize the latest research in bioinformatics published this month. (more…)
Bioinformatics News
This Month in Bioinformatics- Research Updates of October 2020
Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)
Bioinformatics News
This Month in Bioinformatics: Research Updates of September 2020
Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)
Bioinformatics News
This Month in Bioinformatics: Research Updates of August 2020
Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)
Bioinformatics News
This month in Bioinformatics: Research Updates of July 2020
Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)
Bioinformatics News
Inviting Nominations for ‘Top 5 Bioinformaticians in India 2020’
Bioinformatics Review compiles a list of top bioinformaticians every two years. We are inviting nominations for the second edition of this award after the 2018 List. We invite you to contribute to this endeavor by nominating your colleague or friends if you think they can make it to our list.
Nominations start from 20th June 2020 till 15th August 2020. All the nominees will be informed via email on 5th September 2020. We use a well-established ranking method called ScipRank. Our data collection is open-source. ScipRank methodology is publicly available for scrutiny.
Also, we are completing 5th year of success in Bioinformatics Review this year. On this occasion, we are organizing an International Conference on Advanced Research in Bioinformatics 2020. The award will be declared at the conclusion of ConARB 2020 – 3 & 4th Oct 2020).
We invite you to contribute to this endeavor by nominating your colleague or friends. You can also submit your papers, which if accepted, can be presented at the conference.
We have set up a dedicated portal for ConARB 2020 accessible here https://conarb.
To attend or to submit your abstract or to nominate someone, kindly visit this website. Accepted papers will be published in a special issue of Bioinformatics Review.
You must be logged in to post a comment Login