RCSB PDB Judges Looked For …
• Does the overall shape of the model resemble the structure?
• Are differences shown in the two domains at the N- and
• What are the secondary structure elements of this structure?
• How many helices are there?
• What handedness was used to create the helices?
• Does the model hint at what binds to this protein, and where?
Entries were compared to a model generated directly from the
coordinates and a pre-determined rubric.
Protein Modeling State Finals
The state finals will take place March 11, 2008 at Middlesex County
Students may bring their model from the regional competition for
the prebuild section, or they can build a new model. Onsite, they
will build a different section of PDB entry 1cll.
To prepare, teams should definitely explore the resources at education.pdb.org/olympiad.
Questions about the NJSO Protein Modeling trial event should be
sent to firstname.lastname@example.org.
Protein Modeling at the New Jersey
Science Olympiad Regionals
Many models of the structure calmodulin
were built by high school students for the RCSB PDB-sponsored Protein
Modeling event at the Northern and Central New Jersey Science Olympiad.
Science Olympiad tournaments, which take place across the country,
consist of several individual and team events that students prepare
for during the year. Medals are awarded for the top finishers in
each event and for overall performance. During the competition,
teams demonstrate their diverse skills and knowledge in many different
events. In Forensics, teams identify polymers, solids, and fibers
at a crime scene, while in Write It, Do It, students compose a description
of a structure that will be the only guide used by their other team
members to recreate the same shape, sight unseen, with raw materials.
In 2008, Protein Modeling is being held as a trial event at Science
Olympiads in Florida, Indiana, Massachusetts, New Jersey, and Wisconsin.
Team alternates can only participate in trial events, which typically
do not count towards the overall score. In New Jersey, scores in
protein modeling were used in calculating a team’s total score.
This year's protein modeling competition has three components. Students
first build a model of the full calmodulin structure (entry 1cll),
and bring it in the morning to be impounded for judging. Teams are
encouraged to include additions and an abstract that help to illustrate
the function of calmodulin in this model. This model is worth up
to 40 points out of a possible 100.
At the event, teams modeled
a portion of
PDB entry 1cll.
At the event itself, teams build a portion of PDB entry 1cll
with a Mini-Toober (30 points). They also answer questions in a
written exam about the structure, function, importance, and history
of the modeled protein (30 points). For all sections of the event,
students use the Molecule
of the Month, the PDB entry, Jmol (jmol.sourceforge.net/),
and 1cll's Structure Explorer page.
In addition to providing the kits, the Protein Modeling
event in New Jersey is judged by the annotators and computer programmers
of the RCSB PDB. They review each structure by comparing it to a
3D model generated directly from the coordinates and using a model
built directly from the structure's PDB file and a predetermined
rubric that awards points for accurate depictions of the protein's
features. For example, judges look to see if the N- and C-termini
are labeled properly and carefully consider the helices of the model.
They also consider if the main functional and structural features
of the protein are illustrated in the model. The written exam asks
questions based upon the entry's Structure Summary page, the Molecule
of the Month entry, and beyond.
At the Central New Jersey Regional held at Princeton University
(January 8, 2008), Bridgewater-Raritan High School came in first;
South Brunswick High School, second; and West Windsor-Plainsboro
High School North, third.
At the Northern New Jersey Regional held at New Jersey Institute
of Technology (January 17, 2008), Livingston High School came in
first; Westfield High School, second; and Bergen County Academies,
Daniel Zhang and Amy Song with their model of the full structure
of calmodulin. Their on-site model of a section of PDB entry 1cll
received a perfect score
Right: Northern champions Tim Kunisky and Collin Stocks. Their model
was enhanced with masking tape calcium ions. The team from Livingston
High School also came in first place in the overall competition.
The Science Olympiad is an international non-profit
organization devoted to improving the quality of science education,
increasing student interest in science and providing recognition
for outstanding achievement in science education by both students
The 2008 NJSO (www.njscienceolympiad.org)
is presented by the New Jersey Science Teachers Association and the
New Jersey Science Education Leadership Association. Special thanks
to the Center for BioMolecular Modeling at the Milwaukee School of
for the design of this event. Kits similar to those provided for this
event may be purchased from www.3dmoleculardesigns.com.