Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Spring 2012
Number 53


Outreach and Education

San Diego Festival of Science and Engineering

On Saturday, March 24, visitors to the RCSB PDB booth at the San Diego Festival of Science and Engineering's EXPO DAY learned about the basic building blocks of life by building 3D models of DNA and small proteins. They also watched animations of 3D proteins and nucleic acids, and took home posters and other materials about these fascinating structures.

EXPO DAY was the grand-slam-science-finale to a week of big events at San Diego State University, Balboa Park and California State University San Marcos. Activities included building what could be the world's longest DNA model, which was presented at the main stage at EXPO DAY.

Couldn't make it to San Diego? Build models of DNA and the dengue virus at home using PDFs from PDB-101.

Visit PDB-101 for educational resources that explore a structural view of biology

PDB-101's Structural View of Biology promotes a top-down exploration of the PDB.

To start, select from high-level categories describing function: Protein Synthesis, Enzymes, Health and Disease, Biological Energy, Infrastructure and Communication, Biotechnology and Nanotechnology.

The Biological Energy category, for example, involves PDB structures that reveal how cells use chemical energy, light energy, electrical energy, and mechanical energy to power the processes of life. The structures are organized into the following subcategories:

  • Capturing the Energy in Food
  • Photosynthesis
  • Molecular Motors
  • Creating and Capturing Light

Explore biological function and related
structures at PDB-101.
These subcategories link to Molecule of the Month features related to the topic. Capturing the Energy in Food includes articles about structures such as pepsin (an enzyme that digests proteins), lactate dehydrogenase (which creates lactic acid as part of anaerobic respiration), and glycolytic enzymes (used to break down glucose).

Each article then links to special PDB-101 Structure Focus pages which highlight specific entries discussed in the article. These pages describe why the particular structure has been selected as an example, along with an interactive 3D view, sequence display, ligand information, and links to other structure examples discussed in the Molecule of the Month article. For example, the feature on glycolytic enzymes links to Structure Focus pages for all enzymes involved in glycolysis. These Focus pages are streamlined versions of the more complex Structure Summary pages available for all PDB entries.

The Structural View of Biology is a major part of PDB-101, the RCSB PDB resource that packages together materials and tools that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public. Click on the blackboard logo from the top of any RCSB PDB page to enter.

Other areas in PDB-101 include indexes of all Molecule of the Month articles; Educational Resources, with related tools, posters, tutorials, activities, lesson plans, and more; and the Understanding PDB Data reference for exploring and interpreting PDB data.

Modeling Proteins in New Jersey and California at the Science Olympiad

Scenes from protein modeling events across NJ

New Jersey

55 teams from New Jersey high schools demonstrated their understanding of protein structure at recent Science Olympiad competitions, and created 196 protein models along the way.

Science Olympiad tournaments consist of a series of events that test student knowledge in biology, earth science, chemistry, physics and technology. In New Jersey, protein modeling was one of the 25 events for high school teams at the regional and state competitions.

The focus of this year's event uses the example of the discovery and treatment of a rare, disease-causing genetic mutation to explore proteins involved in the regulation of apoptosis. The molecular story behind a mysterious bowel disease, Jmol, and related Molecule of the Month columns are key resources for preparation.

Teams submitted hand-built 3D models of the caspase protein found in PDB entry 1i3o on the morning of the event. The models represented the protein backbone, with additional points awarded added details that highlighted important parts of the structure (such as the defective protein involved in the illness). During the event itself, the students quickly built models onsite (a portion of 1i3o at regionals and PARP protein 3od8 at state) and answered questions on a written exam.

RCSB PDB members judged these competitions, and met with teams at the end of the day to discuss results. Many thanks to the RCSB PDB judges (Luigi Di Costanzo, Sutapa Ghosh, Brian Hudson, Huangwang Yang, Christine Zardecki, and Marina Zhuravleva), the NJ Science Olympiad organizers and volunteers, the host colleges, and to the MSOE Center for BioMolecular Modeling for the materials and design of this event.

Top NJ Results

Protein Modeling state champions from
JP Stevens High School


  1. JP Stevens
  2. Princeton
  3. East Brunswick

Southern Regional:

  1. South Brunswick
  2. West Windsor-Plainsboro North
  3. Moorestown Friends

Central Regional:

  1. JP Stevens
  2. Hillsborough
  3. Princeton II

Northern Regional:

  1. West Windsor-Plainsboro I
  2. West Windsor-Plainsboro South II
  3. Bergen County Academies
Full results are posted at education.pdb.org


Protein modeling was offered for the first time at the San Diego regional on February 18, 2012. The RCSB PDB held workshops to help introduce teams to the event, and members Peter Rose and Michael Gao judged the actual event.

Congratulations to all of the teams that participated!

Protein modeling continues in 2012 at Science Olympiads across the country, culminating at the National Tournament in May. In 2013, the event will go on temporary hiatus as the Science Olympiad rotates in different events in the category of Physical Science & Chemistry.

The RCSB PDB will continue to update education-related news on twitter.com/buildmodels.

Protein Society Honors RCSB PDB Director

Helen Berman is the 2012 Awardee of the Carl Brändén Award of the Protein Society. The Award, sponsored by the Rigaku Corporation, is given to an outstanding protein scientist who has also made exceptional contributions in the areas of education and/or service to the science.

This award recognizes her accomplishments toward enabling a freely available and uniform worldwide archive of 3D structural information for biomedical research and education. Dr. Berman's passion for making structural data accessible and understandable by a broad community has driven the development of the Protein Data Bank into a vital and accessible international resource for biology. In the early 1970s, Berman was a champion of the open access of scientific information; while obvious today, at that time the concept of open access was truly visionary.

The award will be conferred at the 26th Annual Symposium of The Protein Society (August 5-8, 2012) in San Diego, CA. For the full list of awardees, please see proteinsociety.org.

Updated RCSB PDB Training Materials

OpenHelix has updated their free, online training materials to reflect many new RCSB PDB features, including the top bar searching feature with category options, auto-complete feature, improved macromolecule name queries, and PDB-101.

An online narrated tutorial, animated PowerPoint slides, handouts, and training exercises are available for download. Teachers and professors are encouraged to use these resources as classroom content. These files can be accessed from www.openhelix.com/pdb.

Meeting Review Published

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future
Structure 2012 20: 391-396

doi: 10.1016/j.str.2012.01.010