No. 18
Summer 2003

Front Page

Message from the PDB

ADIT Software Available for Download

PDB Deposition Statistics

Submission of Structure Factor Data to the PDB

Clarification of the PDB Policy for "Hold for Publication" (HPUB) Entries

PDB Releases XML Data Files for Beta Test

New Features in Beta Testing

PDB Web Site Statistics

The PDB Talks with Frances C. Bernstein

PDB Focus: DNA Day

PDB Art at Purdue University

Protein Data Bank CD-ROM News

PDB Poster Prize

PDB Molecules of the Quarter: RNA Polymerase, Hemoglobin, and Green Fluorescent Protein (GFP)

PDB Education Corner

Related Links: Software

PDB Job Listings

PDB Members & Statement of Support


© 2003 PDB


PDB Education Corner

PDB's Education Corner 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. Tim Herman, Director of the Center for BioMolecular Modeling at the Milwaukee School of Engineering:

The Center for BioMolecular Modeling (CBM) at the Milwaukee School of Engineering uses rapid prototyping technologies to produce physical models of proteins and other molecular structures based on atomic coordinates obtained from the Protein Data Bank. These physical models are used both by researchers, who find them useful as “thinking tools” and by students who are just beginning to explore the molecular world.

The CBM directs science outreach and professional development programs targeted to both high school science teachers and undergraduate educators ( At the high school level, an NIH-funded SEPA (Science Education Partnership Award) allows us to offer a two-week summer course entitled “Genes, Schemes and Molecular Machines”. In this course, teachers are shown how physical and computer-generated models of proteins can be used to make the molecular world real for their students. Using a recently modified version of RasMol (RP-RasMol), teachers are directly involved in the design and construction of the physical models. In the summer of 2002, a team of six high school science teachers produced the first-ever physical models of the ribosome, based on recently deposited atomic coordinate data ( More recently, we have begun to involve high school students in the design of physical models through our SMART Team program. SMART Teams (Students Modeling A Research Topic) consist of a high school teacher who has participated in our summer course and a group of 3-5 students who work with a local research lab to produce a physical model of the protein under investigation in the lab ( Our first SMART Team, known as Team Anthrax, designed and constructed physical models of the three proteins involved in anthrax pathogenesis in the months immediately following the anthrax attacks in the fall of 2002. Currently, seven SMART Teams are working with researchers in Wisconsin. Plans are underway to replicate this program in other areas including San Diego, upstate New York and Salt Lake City. [For information about how to participate in a SMART Team, contact Prof. Herman at]

At the undergraduate level, the CBM works with undergraduate educators to explore ways in which physical models can enhance the use of molecular visualization tools. With support from an NSF-CCLI award, the Center plans to launch a Summer Modeling Institute at which undergraduate faculty will have access to our physical modeling technologies to design and produce models that will be used in courses on their local campuses. A Model Lending Library has been created to allow any undergraduate educator to borrow models resulting from this project for use in their classroom.

Molecular models for science education--including a DNA Construction Kit--can be obtained from 3D Molecular Designs (3DMD), a recent spin off of the CBM (

A physical model of the p53 tumor suppressor protein from PDB entry 1tsr

PDB ID: 1tsr

Y. Cho, S. Gorina, P.D. Jeffrey, N.P. Pavletich (1994): Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265, p. 346.