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

Summer 2009
Number 42

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Message from the RCSB PDB
Data Deposition
5 Easy Steps for Structure Deposition
Improve the Quality of Your Depositions with SFCHECK
How does an HPUB structure get released?
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
Literature View: Looking at Structures in PubMedCentral
Customizable Structure Summary Pages
MyPDB: Keep up-to-date with new structures... automatically!
Ligand Expo: Searching and Browsing Features
Outreach and Education
Recent and Upcoming Meetings and Presentations
Congratulations to National Tournament Champions
wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe
Looking at Structures: A Resource for Learning About PDB Data
Education Corner
Community Outreach
PDB Community Focus
Gregory Warren, OpenEye Scientific Software, Inc.


Community Outreach

The RCSB PDB hosts local school trips, and gives tours and demonstrations to a wide variety of visitors. This past spring, the RCSB PDB also participated in several outreach programs in our local communities.

San Diego Science Festival

Throughout March and the beginning of April, the San Diego Science Festival (SDSF) brought together students, families, businesses, scientists, and communities for a series of fun (and free) events that highlighted the impact of science and innovation on our lives. Through this program, more than 200,000 people interacted with the San Diego’s local scientific community through various school, evening, and outreach programs.

Small Wonders Cave Tour

High School students and teachers from all over San Diego County visited the University of California, San Diego (UCSD) as part of the Small Wonders program organized by the SDSF and UCSD. This April 1 event offered a day of exploration into the world of nanotechnology and advanced materials.

The RCSB PDB demonstrated the inner workings of proteins in the Calit2 Cave, an immersive environment that features a 5-walled projected virtual reality room with 68-million pixel resolution (for more information about the Cave, see

Students explored the architecture of protein structures, how RNA polymerase transcribes DNA into RNA, and how drugs such as HIV protease inhibitors work. Students and teachers alike were fascinated by both the beauty and the complexity of protein structures. This unique experience certainly sparked a keen interest in science among the students as the organizers had hoped.

Transcription up close: Zooming in on a region in the interior of RNA polymerase.   Exploring secondary structure: Flying through an alpha helix.  
A student takes his classmates on a tour through a protein   Exploring the interior of a transmembrane region of a receptor.  

Expo Day

Using symmetry to build a virus structure at the San Diego Science Festival’s Expo

The finale to the entire SDSF was April 4th Expo Day in Balboa Park. More than 50,000 attendees visited over 200 different booths and watched over 25 science-related performances. The RCSB PDB’s exhibit booth offered hands-on activities, free materials, and demonstrations. In addition to building viruses and exploring proteins with the RCSB PDB, Expo visitors were able to finger paint with algae, play catch with a robot, look through telescopes at sunspots, race remote controlled cars, make test-tube lava lamps, and create musical instruments.




Rutgers Day

On the other side of the country, Rutgers Day was held on April 25 to celebrate all of the exciting activities, programs, and talent at New Jersey's state university. More than 50,000 people attended and participated in free performances, tours, exhibits, hands-on activities, lectures, demonstrations, and the traditional New Jersey events of the Faraday Physics Lecture, Ag Field Day, and the New Jersey Folk Festival. The hosts from the RCSB PDB showed visitors the 3D structures of proteins and built viruses as part of the Department of Chemistry and Chemical Biology’s live experiments and demonstrations.


This large model helps to illustrate the symmetry of the structure.   Virus tattoos were popular with scientists of all ages.  
Visitors could build virus models using toothpicks and marshmallows.      
  Participating RCSB Members: Rutgers • SDSC/SKAGGS/UCSD
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