Software
Installing SMINA on Ubuntu (Linux).

SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on Ubuntu (Linux).
Preparing system
Let’s update and upgrade our system first.
$ sudo apt-get update
$ sudo apt-get upgrade
Downloading SMINA
Download SMINA from here. Change to the directory where you have downloaded the file. Here, we have downloaded in ‘Downloads’. You will see a file named ‘smina.static‘
$ cd Downloads/
Installing SMINA
Give permission to the downloaded file.
$ chmod +x smina.static
Now, you can run this file as shown below.
$ ./smina.static
It will display the usage.
References
- https://sourceforge.net/projects/smina/
Software
AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?
Software
How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
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