SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization . In this article, we are going to install SMINA on Ubuntu (Linux).
Let’s update and upgrade our system first.
$ sudo apt-get update
$ sudo apt-get upgrade
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/
Give permission to the downloaded file.
$ chmod +x smina.static
Now, you can run this file as shown below.
It will display the usage.
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . 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.,. (more…)