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Installing SMINA on Ubuntu (Linux).

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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

  1. https://sourceforge.net/projects/smina/

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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AlphaFill- New algorithm to fill ligands in AlphaFold models.

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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…)

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How to calculate binding pocket volume using PyVol plugin in PyMol?

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How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

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How to generate electron density map using Pymol?

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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.

(more…)

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