Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Spring 2011
Number 49
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Outreach and Education
The Structural Biology of HIV: Online Resources for Understanding
Recent Meetings and Events
NJ Science Olympiad Protein Modeling Results
Papers Published
Education Corner
Richard Tempsick, Academy of Allied Health and Science: Building Protein Structures and the Molecule of the Month

The Structural Biology of HIV: Online Resources for Understanding

A painting of the structural biology of the HIV virus is the focus of new educational materials from the RCSB PDB.

The illustration, by Molecule of the Month author and illustrator David Goodsell, was initially created to commemorate the NIH�s 25th Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and Their Application to Targeted Drug Design that was held March 28-30 in Bethesda, MD. The structural proteins, viral enzymes, and accessory proteins revealed through 25 years of research are highlighted in a poster (PDF) and interactive animation of the virus. Clicking on a protein in the animation reveals a description of the structure and links to the PDB entry.

These features are available from the Educational Resources section of the RCSB PDB. Additional information about HIV-related proteins is found in Molecule of the Month articles on HIV protease, integrase, and reverse transcriptase.

Meetings and Events

Teachers at the NSTA meeting picked up copies of this DNA origami model. Copies can be downloaded from the RCSB PDB's Educational Resources. Students of all ages were introduced to 3D macromolecular structure at the San Diego Science Festival's Expo Day on March 26. Visitors learned about the basic building blocks of life by constructing a model of DNA and translating its sequence into protein. The RCSB PDB's exhibit booth also displayed animations, and offered posters and other materials about these fascinating structures.

RCSB PDB met with researchers and educators while exhibiting at meetings of the Biophysical Society (March 5-9; Baltimore, MD) and the National Science Teachers Association (NSTA; March 9-12; San Francisco, CA). Attendees stopped by the exhibit booth to meet with staff, see demonstrations of new features, and to take home the latest RCSB PDB materials.

In addition to exhibiting, the RCSB PDB sponsored virus model building at the Family Science Days held as part of the annual meeting of the American Association for the Advancement of Science (AAAS; February 17-21; Washington, DC).

The RCSB PDB will be participating at the Annual Meeting of the American Crystallographic Association (May 28-June 2; New Orleans, LA), the Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (July 17-19; Vienna, Austria), and the General Assembly and Congress of the International Union of Crystallography (August 22-30, Madrid, Spain).

The RCSB PDB is also looking forward to the Special Symposium Celebrating the 40th Anniversary of the Protein Data Bank (October 28-30, Cold Spring Harbor, NY) described in this issue's Message from the RCSB PDB.

NJ Science Olympiad Protein Modeling Results

State Top Scoring Teams

1. J.P. Stevens HS (98.75)
2. Princeton (95)
3. Livingston HS (93.5)

Protein modeling state champions from J.P. Stevens High School (Edison): Andy Shi, Joet Bagga, and Sam Zhang
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.

Students demonstrate their knowledge of proteins shown to have reprogrammed adult cells into pluripotent stem cells in this event by building 3D models and completing a written exam.

Teams submitted hand-built 3D models of the zinc finger protein found in PDB entry 2wbu on the morning of the event. The models represented the protein backbone, with additional points awarded for structures with details that highlighted important parts of the structure (such as zinc atoms). During the event itself, the students quickly built a model onsite (POU/HMG/DNA ternary complex found in entry 1gt0 at regionals and homeobox protein Nanog in entry 2kt0 at state) and answered questions on a written exam. The Molecule of the Month, Jmol, and other resources are used to help prepare for this event.

RCSB PDB members judged this competition, and met with teams at the end of the day to discuss results. 48 teams competed in this event, creating 144 models along the way.

Teams that performed well overall at the regional level participate in the state tournament. The top scoring teams at each event were:

Southern Regional Champions: Cherry Hill East High School


Central Regional
1. Hillsborough (88.5)
2. Westfield (86)
3. Union County Vo-Tech (83)

Central Regional Champions (shown at State): Hillsborough High School


Southern Regional
1. Cherry Hill East (85 points)
2. J.P. Stevens (Team 2, 84)
3. Lawrenceville (81)

Northern Regional Champions: West Windsor-Plainsboro South High School


Northern Regional
1. West Windsor-Plainsboro HS South (Team 2, 95.5)
2. West Windsor-Plainsboro HS South (Team 1, 91)
3. Livingston (88.5)
Full results are posted, along with information and resources about this NJ event, at and on Twitter at @buildmodels.

Protein modeling will be one of several events at Science Olympiads across the country. Teams are recognized for their performance in individual events and in the overall tournament. For more information, see

Many thanks to the RCSB PDB judges (Batsal Devkota, Brian Hudson, Buvaneswari Narayanan, Chengua Shao, Huangwang Yang, and Christine Zardecki), 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.

Papers Published

Recent articles include:
  • The Protein Data Bank: exploring biomolecular structure (2010) Nature Education ( 3:39.
  • Precalculated protein structure alignments at the RCSB PDB website (2010) Bioinformatics 26: 2983-2985 doi: 10.1093/bioinformatics/btq572
  • The RCSB Protein Data Bank: redesigned web site and web services (2011) Nucleic Acids Res. 39: D392-D401 doi:10.1093/nar/gkq1021
  • Quality assurance for the query and distribution systems of the RCSB Protein Data Bank (2011) Database: The Journal of Biological Databases and Curation doi: 10.1093/database/bar003
A list of all RCSB PDB publications can be found in the News & Publications section of the website. Citation information is also available.

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