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

Winter 2008
Number 36

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  Data Deposition
• 2007 Deposition Statistics
• ADIT Beta Available for Testing
• New Release of pdb_extract Deposition Tool
• Announcement: Experimental Data Will Be Required for Depositions Beginning February 1, 2008
• Structure Deposition Checklist

Data Query, Reporting and Access
• Website Statistics
• Automated Downloads of PDB Data
• RCSB PDB Focus: Sorting Search Results
• Positions Available at the RCSB PDB

Outreach and Education
• Web Survey: RCSB PDB Educational Resources
• Poster Prize Awarded at AsCA
• Flyers Available in Print and Online
• 2008 Calendar Now Available
• RCSB PDB Paper Cited More Than 5,000 Times

Education Corner
Fruit-flavored Folding by Teresa MacDonald, Director of Education at The University of Kansas Natural History Museum

PDB Community Focus

Protein Modeling at the New Jersey Science Olympiad Regionals



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 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
Questions about the NJSO Protein Modeling trial event should be sent to

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 (, 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.

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 and teachers.

The 2008 NJSO ( 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 Engineering ( for the design of this event. Kits similar to those provided for this event may be purchased from

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