Docking
Beginner’s Guide for Docking using Autodock Vina
We have compiled all articles on docking into a Special Issue. This is a complete guide on molecular docking using Autodock Vina for beginners. It includes blind docking, site-specific docking, installation, output analysis, and so on.
This issue includes the following articles:
- How to install AutoDock Vina on Ubuntu?
- Video tutorial: How to install Autodock Vina on Ubuntu?
- How to perform docking in a specific binding site using AutoDock Vina?
- Video Tutorial: How to perform docking using Autodock Vina
- How to perform blind docking using AutoDock Vina?
- Tutorial: Vina Output Analysis Using PyMol
- Video Tutorial: Autodock Vina Result Analysis with PyMol
- Vina output analysis using Discovery Studio visualizer
- Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions
- How to install Raccoon plugin on Ubuntu for virtual screening using Autodock?
- Raccoon2: A GUI facilitating virtual screenings with Autodock and Autodock Vina
- How to perform virtual screening using Autodock Vina?
- Site-specific docking: Frequently Asked Questions & answers for starters
- MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers
You can also find this special issue on Bioinformatics Review E-Prints.
Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on performing simple protein-ligand site-specific docking using Pyrx. In this article, we are going to perform virtual screening using Pyrx. (more…)
Previously, we provided a tutorial on the installation of idock on Ubuntu (Linux). In this article, we are going to demonstrate the docking of a metal ion (such as Zn, Mg, Fe, etc.,) with a protein using idock. (more…)
idock [1] is a multithreaded software based on Autodock Vina. It is a virtual screening tool for flexible ligand docking. It also supports 27 different chemical elements including zinc, magnesium, iron, calcium, etc. In this article, we are going to install idock on Ubuntu. (more…)
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