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 on protein primary structure; these are somewhat similar to genomic databases that we have seen in Chapter 2, Next-generation Sequencing.

In this chapter, we will mostly focus on processing data from the PDB. We will see 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 in a stable environment. Having said that, the newer mmCIF—slated to replace the PDB format—will also be presented in a later recipe. We will use Biopython and introduce...