June 2015
Intermediate to advanced
306 pages
6h 50m
English
Content preview from Bioinformatics with Python CookbookBecome an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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Introducing Bio.PDB
Here, we will introduce Biopython's PDB module to deal with the Protein Data Bank. We will use three models that represent part of the p53 protein. You can read more about these files and p53 at http://www.rcsb.org/pdb/101/motm.do?momID=31.
Getting ready
You should be aware of the basic PDB data model of Model/Chain/Residue/Atom objects. A good explanation on Biopython's Structural Bioinformatics FAQ can be found at http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ.
You can find this content in the 06_Prot/PDB.ipynb notebook.
Of the three models that we will download, the 1TUP model will be used in the remaining recipes. Take some time to study this model as it will help you later on.
How to do it...
Take a look ...
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