How To Install profbval on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 459 words
Introduction
In this tutorial we learn how to install profbval on Ubuntu.
What is profbval
profbval is:
PROFbval can be useful for both protein structure and function predictions. For instance, a biologist can locate potentially antigenic determinants by identifying the most flexible residues on the protein surface. Additionally, a crystallographer can locate residues that potentially have high experimental B-values.
PROFbval takes the following input, further described on profbval(1):
- a protein sequence in a FASTA file
- secondary structure and solvent accessibility prediction by prof(1)
- an HSSP file
Background: the mobility of a given residue on the protein surface is related to its functional role. Therefore, identification of extremely rigid or flexible residues on the protein surface is helpful for identifying functionally important residues in proteins. A common measure of atom mobility in proteins is B-value data from x-ray crystallography structures. PROFbval is the first tool to predict normalized backbone B-values from amino-acid sequence.
There are three methods to install profbval on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install profbval Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install profbval using apt-get by running the following command:
sudo apt-get -y install profbval
Install profbval Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install profbval using apt by running the following command:
sudo apt -y install profbval
Install profbval 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 profbval using aptitude by running the following command:
sudo aptitude -y install profbval
How To Uninstall profbval on Ubuntu
To uninstall only the profbval package we can use the following command:
sudo apt-get remove profbval
Uninstall profbval And Its Dependencies
To uninstall profbval and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove profbval
Remove profbval Configurations and Data
To remove profbval configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge profbval
Remove profbval configuration, data, and all of its dependencies
We can use the following command to remove profbval configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge profbval
Dependencies
profbval have the following dependencies:
References
Summary
In this tutorial we learn how to install profbval package on Ubuntu using different package management tools: apt, apt-get and aptitude.