Bioinformatics with Python Cookbook

Chapter 7. Using the Protein Data Bank

In this chapter, we will cover the following recipes:

• Finding a protein in multiple databases
• Introducing Bio.PDB
• Extracting more information from a PDB file
• Computing molecular distances on a PDB file
• Performing geometric operations
• Implementing a basic PDB parser
• Animating with PyMol
• Parsing mmCIF files with Biopython

Introduction

Proteomics is the study of proteins that includes the protein function and structure. One of the main objectives of this field is to characterize the 3D structure of proteins. One of the most widely known computational resource in the Proteomics field is the Protein Data Bank, a repository with structural data of large biomolecules. Of course, there are also many databases that focus instead ...