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Docking

Vina output analysis using Discovery Studio visualizer

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The discovery studio (DS) visualizer [1] offers several features for analyzing docking results. In p

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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

Docking

How to install Autodock4 on Ubuntu?

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How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to a

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Docking

What values are considered as good or bad in computational docking?

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After performing computational docking, a question that comes to mind most is “what docking sc

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Bioinformatics Programming

How to sort binding affinities based on a cutoff using vs_analysis.py script?

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How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS)

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Docking

Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

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Virtual Screening using Autodock Vina: Virtual Screening: Frequently Asked Questions & Answers for Starters
Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily perfor

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Docking

[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

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[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins

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Docking

How to generate config file for docking using Autodock Tools?

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How to generate config file for docking using Autodock Tools?
A configuration file is one of the required files for docking using Autodock Vina. In this article,

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Docking

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

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How to install Autodock on Ubuntu (Linux) with CUDA GPU support?
Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during

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Docking

Autodock Vina: Uses & Applications

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Autodock Vina: Uses & Applications
Autodock Vina [1] is one of the most widely used bioinformatics software for computational docking.

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Docking

How to perform virtual screening using Pyrx?

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How to perform virtual screening using Pyrx?
Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on

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Docking

How to perform metal ion-protein docking using idock?

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How to perform metal ion-protein docking using idock?
Previously, we provided a tutorial on the installation of idock on Ubuntu (Linux). In this article,

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Docking

How to install idock on Ubuntu?

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How to install idock on Ubuntu?
idock [1] is a multithreaded software based on Autodock Vina. It is a virtual screening tool for fle

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Docking

How to analyze HADDOCK results using Pymol script generated from PRODIGY?

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How to analyze HADDOCK results using Pymol script generated from PRODIGY?
In one of our previously published articles, we demonstrated protein-protein docking using HADDOCK2.

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Docking

Installing PatchDock on Ubuntu (Linux)

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Installing PatchDock on Ubuntu (Linux)
PatchDock is a docking algorithm that is based on the shape complementarity principle [1,2]. It perf

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Docking

Protein-protein docking using HADDOCK2.4 web server

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Protein-protein docking using HADDOCK2.4 web server
HADDOCK2.4 web server (https://bianca.science.uu.nl/haddock2.4/) [1] is used for protein-protein doc

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Docking

How to perform site-specific docking using Pyrx?

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How to perform site-specific docking using Pyrx?
Pyrx [1] is a virtual screening software that allows the docking of multiple ligands with a target p

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Software

How to install sdsorter on Ubuntu (Linux)?

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How to install sdsorter on Ubuntu (Linux)?
sdsorter is a tool that helps in the easy manipulation of SDF files. It takes a single file as input

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Docking

Video Tutorial: How to use vs_analysis Python script for virtual screening result analysis of Autodock Vina?

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How to use vs_analysis python script for virtual screening result analysis of Autodock Vina
This is a demonstration video of our previously mentioned Python script (vs_analysis.py) for virtual

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Docking

Basic Methodology to Predict Antigen-Antibody Interactions in silico

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antigen-antibody interaction prediction
Antigen-antibody interactions play an important role in protecting our body from foreign molecules.

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Docking

What is Virtual Screening in Bioinformatics?

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What is virtual screening in bioinformatics?
If you are a beginner in the field of bioinformatics, you must have heard of the term “virtual

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Docking

Blind Docking vs Site-specific Docking

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Blind docking vs site-specific docking
We have provided several tutorials on docking including both types: blind docking & site-specifi

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