PDB COMMUNITY FOCUS

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
C-termini?

• 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.

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Protein Modeling State Finals

The state finals will take place March 11, 2008 at Middlesex County College.

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 buildmodels@deposit.rcsb.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, third.

Left: Bridgewater-Raritan’s 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.