Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank

Summer 2010
Number 46

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Data Deposition and Annotation
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Use Ligand Expo When Depositing Structures with Ligands
Deposition Statistics
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Outreach and Education
Recent and Upcoming Meetings and Presentations
Congratulations to National Tournament Champions
Papers published
Screencasts and Tutorials Demonstrate RCSB PDB Features
Education Corner
Phil McFadden: Protein Portraits

Outreach and Education

Recent and Upcoming Meetings and Presentations

More than 75,000 people came to the Rutgers Day showcase of the varied resources, departments, and people at the university. Visitors to the RCSB PDB�s table with the Department of Chemistry and Chemical Biology were able to learn about protein structure next to experiments and demonstrations of how chemistry impacts the food we eat, the air we breathe, the cars we drive, and the medicines we take.

Virus models were built using marshmallows and toothpicks, or with the paper template available for download from the Molecule of the Month feature on the dengue virus.

The RCSB PDB exhibited along with the PSI Structural Genomics Knowledgebase at the American Society for Biochemistry and Molecular Biology's Annual Meeting (April 24-28, Anaheim, CA), which was held in conjunction with the Experimental Biology conference.

Booth visitors at the Experimental Biology meeting were able to meet with RCSB PDB staff, explore new website features, and pick up the How Do Drugs Work? poster.

A pop-up edition of the Art of Science exhibit was staged as part of Rutgers' Alumni Weekend (May 14). The RCSB PDB's traveling exhibit includes large-scale depictions of proteins, including images and text from the Molecule of the Month series. To learn more about this program, please contact

As part of Alumni weekend, the Art of Science exhibit was installed at Rutgers and included a lecture about protein structure and scientific art.
photo credit: Jon Horowitz

The RCSB PDB will participate at the 24th Annual Symposium of The Protein Society (August 1-5; Boston, MA) and in the PDB and Chemistry Symposium at the 240th National Meeting of the American Chemical Society (August 22 - 26; Boston, MA).

Congratulations to the National Protein Modeling Champions

Troy High School's model of hemagglutinin.

Teams built models onsite using Jmol as a guide.
In the 2010 Science Olympiad protein modeling trial event, high school teams were asked to demonstrate their understanding of hemagglutinin, neuraminidase, and how protein structure related to the H1N1 influenza virus.At these competitions held at regional and state levels, teams brought a model of hemagglutinin to the event to be judged, built a portion of a protein at the onsite competition, and answered questions on a written exam about H1N1.

The National Science Olympiad championships were held May 20-22 at the University of Illinois at Urbana-Champaign. Out of 44 participating teams, Troy High School from California won the protein modeling event in a tie break.

The protein modeling event focuses on structures highlighted by the Molecule of the Month series. The RCSB PDB also sponsors the events held in New Jersey. Information and resources can be found at and

The event is organized nationally by the MSOE Center for BioMolecular Modeling.

Full results, rubrics, and photos have been posted at For the past few years, protein modeling has been a trial event offered in a few states. In 2011, protein modeling will be available as a full event offered to all states.

Protein Modeing Event at the National Science Olympiad
May 20-22, 2010
University of Illinois at Urbana-Champaign

1st Place
Troy High School, CA

2nd Place:
West Windsor-Plainsboro South High School, NJ

3rd Place
New Trier High School, IL

Congratulations to all of teams who participated!

Questions from the Protein Modeling Event

Since our body develops immunity to the bacteria and viruses we are exposed to, whether through illness or vaccine, why do we need to get a flu shot every year?

Influenza strains that are resistant to the antiviral Tamiflu have been emerging, which means that treating patients with Tamiflu is becoming less effective against the viral infection. What is the key mutation in neuraminidase that leads to resistance to the antiviral? What is significant about this mutation that prevents Tamiflu from working effectively?

Hemagglutinin undergoes a major conformational change after the virus has been taken into the host cell through endocytosis. What triggers this conformational change and why is this change so essential to the function of hemagglutinin?

Papers Published

Articles describing how open access literature is integrated with the RCSB PDB and how scientific illustrators can utilize the PDB data and the RCSB PDB resource have been published:

  • Integration of open access literature into the RCSB Protein Data Bank Using BioLit.
    Andreas Prlić, Marco A Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T Yukich, Peter W Rose, Philip E Bourne, J Lynn Fink
    BMC Bioinformatics (2010) 11:220. doi:10.1186/1471-2105-11-220

  • Getting the Most Out of the Protein Data Bank
    David S. Goodsell (2009) The Journal of Biocommunication 35: E52-E57.

Screencasts and Tutorials Demonstrate RCSB PDB Features

Short, online narrated videos describe how to use ligand searching and website customization tools. The screencasts currently offered at demonstrate:

  • Ligand searching: Using the MarvinSketch applet
  • Ligand searching: Advanced MarvinSketch features
  • Ligand searching: Using SMARTS features
  • Ligand searching: Loading a PDB chemical component
  • Customizing Structure Summary pages using Widgets
  • Tour of the left hand menu

For a more detailed introduction to the features and functionality of the RCSB PDB, comprehensive training materials are available at The training tools include an online narrated tutorial that demonstrates basic and advanced searching, report generation, exploring individual structures, and many other research and education tools. The full tutorial runs for about an hour, and can be navigated by specific chapters.

The animated PowerPoint slides used as a basis for the tutorial can be downloaded, along with slide handouts and exercises. These materials are freely available for teachers and professors to create classroom content.

To accompany the online tutorial, OpenHelix offers free Quick Reference Cards for the RCSB PDB that highlight search strategies, features and functionality. The cards can be ordered at at no cost; shipping is free within the United States.

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