Google Colab Setup for Biopython

A simplified CADD pipeline often looks like the following

Target protein sequence (FASTA) → Structure (AlphaFold / homology / PDB, or already available 3D structure) → Docking / Virtual screening → Molecular Dynamics Simulation → Analysis.

In this Tutorial, we are going to focus on the first block, which is the protein, and how to manipulate a protein sequence and other important modifications.

You can access the Google Colab here; it contains all the code used in this tutorial: Google Colab.

Google Colab Setup

Open a new notebook

Click New Notebook.

To run the code present in a cell, press Shift + Enter (Figure 1)

Install Biopython

Copy/paste into a code cell, pip is the installer. -q means “quiet” (less output) (Figure 2). 

Code:

!pip -q install biopython 

Confirm if Biopython is installed

If a version prints without errors, you’re ready (Figure 3). 

Copy/paste into a code cell

Code:

import Bio

print("Biopython version:", Bio.__version__)

Welldone you just finished the installation of Biopython, Let move to the next section.