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

Spring 2009
Number 41

Home | Newsletter Archive | PDF Version
Message from the RCSB PDB
Data Deposition
PDB Archive Version 3.15 Released
Papers Published
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
New Feature: Receive Email Alerts When New Structures Match Your Queries with MyPDB
Time-stamped Copies of PDB Archive Available via FTP
Outreach and Education
New Jersey Science Olympiad: Protein Modeling
Education Corner
Gavin Whittaker, Ph.D.,
Molecular Models: Tangible Representations of the Abstract
PDB Community Focus
GaŽl McGill, Ph.D., and Graham Johnson, Molecular Animators

Outreach and Education

New Jersey Science Olympiad: Protein Modeling

At Science Olympiad tournaments, teams participate in a variety of events ranging from Egg-O-Naut to Herpetology. Placement in individual events counts towards placement in the overall competition. In New Jersey, protein modeling was a trial event for high school students at all three regional tournaments and at the state finals.

Before the day of competition, teams built a model of the full ribonuclease structure based on PDB ID 1rta. In this model, teams are encouraged to include "additions" that help tell the functional story of ribonuclease. They also provide an abstract/key that describes features highlighted in their model.

Models built before the competition were judged for accuracy
and how well they told the functional story of the molecule.

At the event itself, teams have 50 minutes to build a section of an assigned PDB structure and answer questions about the structure, function, importance, and history of ribonuclease. For all sections of the event, students are encouraged to use the Molecule of the Month, the PDB file, Jmol and the Structure Explorer page. Resources to help students prepare for the event are available at, including a video that demonstrates how to build a 3D model of a zinc finger.

Top Results at the 2009 NJSO Tournaments
First Places
Second Place
Third Place
March 17
High School
West Windsor-Plainsboro
High School South
High School
January 15
High School
High School
January 8
High School
West Windsor-Plainsboro
High School South
High School

January 10

Moorestown Friends School
Regional High School

Congratulations to all participating teamsĖthere were many great models, abstracts, and responses to the written exam. Special thanks to our judges from the RCSB PDB, the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.

All 2009 results, pictures, and tips for future competitions can be found at

State Champions
(and winner of the Central Regional)
from Bridgewater Raritan High School.
The Southern Regional Champions from the MATES Academy team built a portion of ribonuclease using the RCSB PDB website site and MiniToobers (from 3D Molecular Designs,

A judge described how the models were scored with the Northern Regional Champions from Westfield High School. RCSB PDB annotators judged the protein models built onsite for accuracy.
  Participating RCSB Members: Rutgers • SDSC/SKAGGS/UCSD
E-mail: • Web: • FTP:
The RCSB PDB is a member of the wwPDB (
©2009 RCSB PDB