How To Install concavity on Kali Linux

In this tutorial we learn how to install concavity on Kali Linux. concavity is predictor of protein ligand binding sites from structure and conservation

Introduction

In this tutorial we learn how to install concavity on Kali Linux.

What is concavity

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 ways to install concavity on Kali Linux . 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 Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove concavity

Remove concavity Configurations and Data

To remove concavity configuration and data from Kali Linux 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 using different package management tools like apt, apt-get and aptitude.