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 Focus: David Goodsell and the Molecule of the Month

The Molecule of the Month series explores the functions and significance of selected biological macromolecules for a general audience. These features, written and illustrated by Dr. David S. Goodsell of The Scripps Research Institute, are available at

Recently, the PDB interviewed Dr. Goodsell to find out how he creates these beautiful and informative works of art and science.

PDB: How did this idea emerge initially?
Goodsell: When I started, I wanted to create a friendly doorway to the PDB. The PDB contains many interesting structures, but it can be daunting to people who aren't experienced with atomic coordinates and molecular viewers. One great challenge is the sheer magnitude of the PDB. For instance, if you are interested in hemoglobin, you are faced with dozens of structures, and it may be difficult to choose one for further exploration. My goal these days is to present a general introduction to each molecule, and then give a few suggestions for PDB entries that show the major features of the molecule. A place for visitors to start in their own exploration of these fascinating molecular machines.

PDB: How do you create the illustrations?
Goodsell: Most of the pictures are created with a computer program that I developed back when I was doing postdoctoral work with Dr. Art Olson here at The Scripps Research Institute. I've been using this style of illustration--with flat colors and black outlines--for about 10 years now. I like the way that this style simplifies the molecule, giving a feeling for the overall shape and form of the molecule, but at the same time you can still see all the individual atoms. On the last page of each Molecule of the Month--"Exploring the Structure"--I always use RasMol, to give visitors an idea of the kinds of pictures that they can create themselves with off-the-shelf software.

Proteins are challenging subjects to illustrate. I try to find views that show off the unusual features of the molecules. I like to work with molecules where there is a clear relationship between the structure and the function, such as the way that the ribosome clamps around the messenger RNA or the power stroke motion of myosin. I am also fascinated by the beautiful symmetry of proteins, and always create pictures that highlight this symmetry. Every Molecule of the Month is a new adventure.

PDB: How do you select the featured structures?
Goodsell: I try to pick molecules that play a familiar role in human life and health. My favorites are molecules where we can see how the molecular structure and function are directly related to something that we experience in our lives. Myosin is a good example--we can easily imagine those countless little engines crawling up actin as we bend our arm. For each new Molecule of the Month, I try to pick 4-5 PDB entries that, in my opinion, best show the functional features that I am describing.

PDB: Has it been popular?
Goodsell: Well, I hope so! I have gotten a bunch of great letters from visitors--students, teachers, researchers, and all sorts of other people. I always like it when people use my pictures in their own assignments or presentations, to aid in their own exploration of the subject.

PDB: What do you plan for the future?
Goodsell: Lots more molecules! I'm planning a new column on hemoglobin with Dr. Shuchismita Dutta (Rutgers-PDB), who helped out on the one on potassium channels a few months ago--look for it later this Spring. I don't have any plans to enlarge the Molecule of the Month--the PDB is growing too fast to think of doing anything more comprehensive. I'm planning to keep it small and informal--a new tidbit each month.

Dr. David S. Goodsell
Dr. David S. Goodsell