Docking
Vina output analysis using Discovery Studio visualizer

Docking
How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to a
Docking
What values are considered as good or bad in computational docking?

After performing computational docking, a question that comes to mind most is “what docking sc
Bioinformatics Programming
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)
Docking
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily perfor
Docking
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
![[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn.jpg)
Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins
Docking
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,
Docking
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
Docking
Autodock Vina: Uses & Applications

Autodock Vina [1] is one of the most widely used bioinformatics software for computational docking.
Docking
How to perform virtual screening using Pyrx?

Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on
Docking
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,
Docking
How to install idock on Ubuntu?

idock [1] is a multithreaded software based on Autodock Vina. It is a virtual screening tool for fle
Docking
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.
Docking
Installing PatchDock on Ubuntu (Linux)

PatchDock is a docking algorithm that is based on the shape complementarity principle [1,2]. It perf
Docking
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
Docking
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
Software
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
Docking
Video Tutorial: 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
Docking
Basic Methodology to Predict Antigen-Antibody Interactions in silico

Antigen-antibody interactions play an important role in protecting our body from foreign molecules.
Docking
What is Virtual Screening in Bioinformatics?

If you are a beginner in the field of bioinformatics, you must have heard of the term “virtual
Docking
Blind Docking vs Site-specific Docking

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