DockingAnalyzer.py: A New Python script to Identify Ligand Binding in Protein Pockets.
High-throughput virtual screening (HTVS) is a pivotal technique in drug discovery that…
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://bioinformaticsreview.com/wp-content/uploads/2023/10/dockingpie1.jpg)
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
DockingPie is a PyMOL plugin to perform computational docking within PyMOL .…
How to install the DockingPie plugin on PyMOL?
DockingPie is a plugin of PyMOL made to fulfill the purpose of…
Common mistakes made during computational docking.
Computational docking is not a trivial task once we avoid making some…
What values are considered as good or bad in computational docking?
After performing computational docking, a question that comes to mind most is…
Installing SMINA on Ubuntu (Linux).
SMINA is a fork of AutoDock Vina supporting better scoring function and…
![[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn.jpg)
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
Proteins containing zinc atoms are docked in a different way than that…
How to generate config file for docking using Autodock Tools?
A configuration file is one of the required files for docking using…
How to install Autodock on Ubuntu (Linux) with CUDA GPU support?
Autodock is most widely used for docking. To accelerate the docking process,…
Autodock Vina: Uses & Applications
Autodock Vina is one of the most widely used bioinformatics software for…
Generating multiple low-energy conformers using Avogadro
In our previous article, we generated multiple conformers using OpenBabel. In this…
How to generate multiple conformers of a ligand using OpenBabel?
OpenBabel offers several functions including file format conversion, generation of 3D structures…
How to perform metal ion-protein docking using idock?
Previously, we provided a tutorial on the installation of idock on Ubuntu…
Installing Raccoon2 plugin on Windows.
We have previously provided an article on the installation of the Raccoon2…
How to analyze HADDOCK results using Pymol script generated from PRODIGY?
In one of our previously published articles, we demonstrated protein-protein docking using…
Installing PatchDock on Ubuntu (Linux)
PatchDock is a docking algorithm that is based on the shape complementarity…
How to perform site-specific docking using Pyrx?
Pyrx is a virtual screening software that allows the docking of multiple…
Where to find Docking and MD simulation software?
Docking and simulation are two of the methods that are most widely…
Most widely used software for docking results image generation
Computational docking is an important technique in bioinformatics. The docking result interpretation…
What does the coordinates mean in docking?
Researchers working in the field of bioinformatics are well-aware of the word…