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

Spring 2010
Number 45

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Message from the RCSB PDB
Data Deposition
Deposition Statistics
wwPDB News: Changes to the wwPDB Policy for Depositing Polypeptide Structures
wwPDB News: Initial Release REVDAT Dates
Data Query, Reporting and Access
Website Statistics
Improved Ligand Searching
Comparison Tool for Exploring Sequence and Structure Alignments
Advanced Search: Sequence Motif
Time-stamped Copies of PDB Archive Available via FTP
Outreach and Education
Online Narrated Tutorial Demonstrates How to Use the RCSB PDB
Poster Download: How Do Drugs Work?
NJ Science Olympiad Protein Modeling Results
Recent and Upcoming Meetings and Events
Education Corner
Robert C. Bateman, Jr. and Paul A. Craig: A Proficiency Rubric for Biomacromolecular 3D Literacy

Outreach and Education

Online Narrated Tutorial Demonstrates How to Use the RCSB PDB

Comprehensive training materials to introduce users to the features and functionality of the RCSB PDB are now freely available at The new training tools include an online narrated tutorial that demonstrates basic and advanced searches, how to generate reports, the different options for exploring individual structures, and many of the resources and tools available at the RCSB PDB for research and education. The full tutorial runs for about an hour, and can be navigated by specific chapters.

The animated PowerPoint slides used as a basis for the tutorial can be downloaded, along with slide handouts and exercises. These materials are freely available for teachers and professors to create classroom content.

OpenHelix has also created Quick Reference Cards for the RCSB PDB that highlight search strategies, features and functionality. The cards can be ordered at at no cost; shipping is free within the United States.

In addition to viewing the narrated tutorial, users can download slides and exercises that illustrate how to use the RCSB PDB searching and reporting functions at

Poster Download: How Do Drugs Work?

A new poster that explores different kinds of protein-drug structures found in the PDB archive is available for download as a poster (26 x 38") and flyer (8 1/2 x 11").

How Do Drugs Work? was inspired by the success and enduring popularity of 2002's poster on Molecular Machinery: A Tour of the Protein Data Bank. That poster, which depicts many PDB structures drawn to scale, is also available.

Written and illustrated in a style similar to the Molecule of the Month series, the poster uses PDB structures to discuss antibiotics and antivirals, chemotherapy, drug metabolism, drugs of signaling proteins, and lifestyle drugs.

All posters and flyers are available from the RCSB PDB's Educational Resources page. Printed copies will be distributed at scientific and educational meetings.

NJ Science Olympiad Protein Modeling Results

High school teams across New Jersey demonstrated their understanding of hemagglutinin, neuraminidase, and protein structure at Science Olympiad competitions held across the state.

At the RCSB PDB-sponsored protein modeling trial event, teams submitted their hand-built 3D models of a hemagglutinin protein with an abstract to be judged by staff from the RCSB PDB. These models were enhanced with different features to help tell the story of hemagglutinin's function. At the competition, teams quickly built a model of a selected protein region using Jmol and completed a written exam with questions about protein structure and influenza. Teams used the Molecule of the Month and other RCSB PDB resources to help prepare for this event. 35 teams competed in this event at three regional tournaments in January.

The top scoring teams were:

Southern Regional
January 9, 2010
Camden County College

1. Cherry Hill High School East
2. MATES Academy
3. The Lawrenceville School


Cherry Hill East and their prebuild model of hemagglutinin. A rubric was used to award points for the accuracy of the model and for the addition of materials that illustrated the function of the protein.


Central Regional
January 12
Union County College

1. South Brunswick
2. Westfield
3. Hillsborough

The team from South Brunswick marked the beta sheets in their model after viewing them in Jmol.


Northern Regional
January 14
New Jersey Institute of Technology

1. West Windsor Plainsboro South
2. Livingston
3. Princeton

Annotator Marina Zhuravleva reviews the scoring for West Windsor Plainsboro South's prebuild model with the team.

At the State Finals (March 16, Middlesex County College), where the top scoring teams at all NJSO events compete, 24 teams participated. The top scores went to first place West Windsor Plainsboro North, second place West Windsor Plainsboro South, and third place New Providence.

Special thanks to our all of our judges from the RCSB PDB, the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for developing this event nationwide.

Information and resources about this event are posted at and on

For more information on the NJ Science Olympiad please see

The state champions from West Windsor Plainsboro High School North.


Recent and Upcoming Meetings and Events

John Westbrook at the Biophysical Society.

Virus building at SDSF.
The RCSB PDB presented along with the PSI SGKB at the 54th Annual Meeting of the Biophysical Society (February 20-24) in 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. A poster on Education and Outreach at the RCSB Protein Data Bank was also presented by Christine Zardecki.

At the National Science Teachers Association's National Conference (March 18-21) in Philadelphia, PA, the RCSB PDB met with teachers at levels ranging from middle school to college. Teachers new to the resource were enthusiastic about incorporating features such as the Molecule of the Month in their classes, while current users were pleased to pick up materials such as the How Do Drugs Work? poster.

RCSB PDB staff introduced students of all ages to protein structure and function by building 3D models of virus structures at Princeton's Science and Engineering Expo (March 18) and the San Diego Science Festival Expo Day (SDSF; March 27).

Future meetings this summer include the 18th Annual International Conference on Intelligent Systems for Molecular Biology (July 11-13, Boston, MA); the American Crystallographic Association's meeting (July 24-29, Chicago, IL); the Protein Society (August 1-5, San Diego, CA), and a half day symposium on The PDB and Chemistry at the American Chemical Society's National Meeting & Exposition (August 22-26, Boston, MA).


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