Using the Protein Data Bank

Proteomics is the study of proteins, including their function and structure. One of the main objectives of this field is to characterize the three-dimensional structure of proteins. One of the most widely known computational resources in the proteomics field is the Protein Data Bank (PDB), a repository with the structural data of large biomolecules. Of course, many databases focus on protein primary structure instead; these are somewhat similar to the genomic databases that we saw in Chapter 2, Getting to Know NumPy, pandas, Arrow, and Matplotlib.

In this chapter, we will mostly focus on processing data from the PDB. We will look at how to parse PDB files, perform some geometric computations, and visualize molecules. We will use the old PDB file format because, conceptually, it allows you to perform most necessary operations within a stable environment. Having said that, the newer mmCIF slated to replace the PDB format will also be presented in the Parsing...