How To Install concavity on Ubuntu 22.04
Introduction
In this tutorial we learn how to install concavity
on Ubuntu 22.04.
What is concavity
concavity is:
ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
ConCavity takes as input a PDB format protein structure and optionally files that characterize the evolutionary sequence conservation of the chains in the structure file.
The following result files are produced by default:
- Residue ligand binding predictions for each chain (*.scores).
- Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb).
- Pocket prediction locations in a DX format file (*.dx).
- PyMOL script to visualize the predictions (*.pml).
There are three methods to install concavity
on Ubuntu 22.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install concavity Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install concavity
using apt-get
by running the following command:
sudo apt-get -y install concavity
Install concavity Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install concavity
using apt
by running the following command:
sudo apt -y install concavity
Install concavity Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install concavity
using aptitude
by running the following command:
sudo aptitude -y install concavity
How To Uninstall concavity on Ubuntu 22.04
To uninstall only the concavity
package we can use the following command:
sudo apt-get remove concavity
Uninstall concavity And Its Dependencies
To uninstall concavity
and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove concavity
Remove concavity Configurations and Data
To remove concavity
configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge concavity
Remove concavity configuration, data, and all of its dependencies
We can use the following command to remove concavity
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge concavity
References
Summary
In this tutorial we learn how to install concavity
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.