Biopython for Computer-Aided Drug Design (CADD) I

What You Need to Know Before Starting

This tutorial is written for someone who:

• Has never used Biopython before

• May not know what a FASTA file is

• Wants to do CADD (docking, structure modeling, MD) and needs the right protein sequence

What is Biopython?

Biopython is a Python toolkit that provides reliable, biology-aware tools to work with sequences and some biology file formats.

In CADD, most workflows need a protein sequence (FASTA) and a protein structure (PDB/mmCIF) when dealing with structure-based drug design.

If the sequence/protein that is used is wrong (wrong isoform, truncated, wrong chain), then the following errors can occur:

• The structure model can be wrong.

• The binding pocket can shift.

• Docking and MD results become unreliable.

The following are the Biopython core concepts you will use in this tutorial.

1. Seq — a biological sequence object (DNA/RNA/protein)

2. SeqRecord — a sequence + metadata (ID, description)

3. SeqIO — reading/writing files (FASTA, GenBank, etc.)

You need to think of the following concept like this:

• Seq = the sequence itself

• SeqRecord = the sequence with a label

• SeqIO = the file reader/writer.