This document provides some basic information about an important, free resource for viewing biological molecules – the Protein Data Bank or PDB. The PDB is a website where people who have solved structures of biological molecules (proteins, nucleic acids, etc.) can deposit their data for the public to examine. While the PDB has many, many different features, this document focuses on ways for new users to get started with this resource and provides examples of exercises I have asked students to do in my biochemistry and bioinorganic courses.
The goal of this Learning Object is to provide the resources necessary to find a molecule on the PDB website, understand what information is provided, use one of the viewing programs to explore the structure of the molecule, and generate their own pictures of the structure.
As mentioned in the attached Word document, I check to see that students are doing the tutorials and using the viewing programs by asking them to turn in answers to questions about the information on the site as well as some figures they have generated of their molecule. Most often, I grade this homework with a check, check-plus, check-minus system.
Generally most students are able to find the required information on the PDB site. Using the viewing program can be hard for some. I generally sit down with those students and show them how use one of the simpler viewing programs. Some students become very adept at the viewing programs and can make some amazing figures.