No. 17
Spring 2003

Front Page

Message from the PDB

PDB Deposition Statistics

PDB Annotation Manual Online in PDF and PostScript Formats

PDB Focus: ADIT Annotators

New Features Available for Beta Testing: Biological Unit, Curated (Beta) mmCIF Files, Redundancy Reduction Cluster Data

New Features on the Structure Explorer Pages of the PDB Web Site: Author and Ligand Searches, BioMagResBank Links

PDB Focus: Redundancy Reduction Capability

PDB Focus: Maintaining a Local PDB FTP Mirror Site

PDB Focus: Weekly Updates to the PDB

PDB Web Site Statistics

Structural Bioinformatics Book Includes Chapters on the PDB

PDB Paper Published in Nucleic Acids Research

New Distribution Procedure for Protein Data Bank CD-ROM Sets

PDB at the Biophysical Society Meeting

PDB Focus: David Goodsell and the Molecule of the Month

PDB Molecules of the Quarter: Serum Albumin, Potassium Channels, and lac Repressor

PDB Education Corner

Related Links: Education

PDB Job Listings

PDB Members & Statement of Support


© 2003 PDB


PDB Education Corner

PDB's Education Corner is a new column that features a different teacher each quarter, offering an account of how he or she uses the PDB to educate students. Educators will find this information useful to inspire their own courses and methods of teaching that incorporate the PDB.

This quarter's column is by Prof. Gale Rhodes, from the University of Southern Maine:

Students in my introductory biochemistry course learn how to visualize and study macromolecules by computer graphics at the same time they learn the basics of protein structure. They learn how to obtain macromolecular models from the Protein Data Bank and to analyze their structure with Deep View (aka Swiss-PdbViewer). After learning how to use Deep View by way of a hands-on workshop and a web tutorial (, they pick a protein for individual study, obtain it from the Protein Data Bank, get to know its structure, and write a structural description illustrated with views in a Deep View project file. Throughout the rest of the course, students work problems from a graphics problems supplement. Students must obtain PDB models and study them with Deep View in order to solve the problems. I also use Deep View and PDB models throughout the course to illustrate all aspects of macromolecular structure and function. Finally I am currently developing an introduction to bioinformatics for the second semester of my biochemistry course. This teaching unit, a study of human opsins, will entail a FASTA search of the PDB for opsin structures (and finding bovine rhodopsin, no doubt), and will culminate with homology modeling of a human opsin, using a search of the ExPDB database for templates.

In addition to this use of PDB models in my teaching, I have a little outreach project called "The Molecular Level: Molecular Graphics Training for Students, Teachers, and Researchers". Through this program, I provide hands-on workshops in molecular graphics to area researchers, students in other courses at USM, and advanced-placement biology and chemistry high-school students and teachers. Workshop participants get a hands-on introduction in which they learn how to obtain models from the PDB and study them with Deep View. They can then use my tutorial to follow up the workshop.

For more information about my use of graphics in introductory biochemistry, see "Molecular Graphics Manifesto: Why and How to Integrate Molecular Graphics into Introductory Biochemistry", at

To see my graphics exercises for a biochemistry course, see "Learning Biochemistry with Deep View: A Gallery of Graphics Exercises for Introductory Biochemistry", at

To see typical workshop outlines and other resources of "The Molecular Level" outreach program, go to

My introduction to bioinformatics is under development. You can see what I've done so far (PDB and homology modeling parts not done yet) at