RCSB PDB's Molecule of the Month series explores the functions
and significance of selected biological macromolecules for a general
audience. These features, produced by Dr. David S. Goodsell (The
Scripps Research Institute and the RCSB PDB), are available
Recently, the RCSB 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
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
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
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
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
PDB Focus: David Goodsell and the Molecule of the Month,
1, 2003 PDB News.
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The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.