Computing molecular distances on a PDB file

Here, we will find atoms closer to three zincs in the 1TUP model. We will consider several distances to these zincs. We will take this opportunity to discuss the performance of algorithms.In this recipe, we will use the Biopython PDB module to parse and interact with the structure of a protein. We’ll learn how to define a simple distance function to see how close various atoms in the model are from key points in the structure. Finally, we’ll dive into some compute optimization and see how we can make our calculations faster!Knowing how to calculate the molecular distances between various atoms in the protein structure model is important and can be useful for several reasons. First off, it can be used to check various constraints to validate the accuracy of the model. It can be especially important in Protein Engineering when we need to try and find what residues might be close to the Active Site. It can also be used to help understand...