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

Spring 2008
Number 37

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Data Deposition
• sf-convert: A Format Conversion Tool for Structure Factor Files
• EmDep2: Deposit EM Maps at the MSD-EBI or RCSB PDB
• 2008 Deposition Statistics
• Data Processing Versioning Procedures

Data Query, Reporting and Access
• Website Statistics
• PDB Statistics
• Time-stamped Copies of PDB Archive Available via FTP

Outreach and Education
• RCSB PDB Celebrates Teaching, Learning, and More
• Protein Sculptures on Display at Rutgers
• Papers Published

Education Corner
Moving Pictures: Using Chimera to Make Molecular Multimedia for the Classroom by Dr. Jeramia Ory, Kings College

PDB Community Focus

Dr. Christine Orengo, University College London


RCSB PDB Celebrates Teaching, Learning, and More

The RCSB PDB exhibits at meetings to get feedback from our users about the resource.

Recent education and outreach activities have included:

  • Annotators made models of virus structures with local middle school students as part of Princeton University's Science and Engineering Expo on March 19. The models included marshmallow and toothpick representations of the viral shell and paper models of the dengue fever virus.
  • An exhibit booth was also held at the Teaching & Learning Celebration in New York, NY, March 7-8. Educators and policy makers from the Tri-State area came to the booth to learn about protein structures, the RCSB PDB, and to take home tRNA tattoos.
  • The RCSB PDB exhibited at the Biophysical Society's annual meeting (February 2-6; Long Beach, CA).




Protein Sculptures on Display at Rutgers

Cycloviolacin (2007, copper-coated steel, 24" x 32" x 36")

Sculptures and photographs by Julian Voss-Andreae were on display at the Rutgers Student Center in New Brunswick, New Jersey in February.

Voss-Andreae's unique sculptures are designed to tell stories about hemoglobin, collagen, and other structures essential to life.

Julian Voss-Andreae is a German-born sculptor based in Portland. He graduated from the Pacific Northwest College of Art (PNCA) in 2004 with a BFA in sculpture. While still at PNCA, Voss-Andreae developed a novel kind of sculpture based on the structure of proteins, the building blocks of life. Voss-Andreae's work has been commissioned internationally and has been highlighted in journals such as Leonardo and Science.

Photographs of Voss-Andreae's sculptures are part of the RCSB PDB's Art of Science traveling exhibit, which also features images available from the RCSB PDB website and the Molecule of the Month. For more information on hosting this exhibit, please contact

The next stop for the cycloviolacin sculpture is the Art and Mathematics: The Wonders of Numbers exhibit at The Heckscher Museum of Art, April 12 - June 22, 2008, in Huntington, NY.

Julian Voss-Andreae:

The Heckscher Museum:

Papers Published

The PDB archive, which began in 1971 as a handwritten petition signed by crystallographers, has developed into an online biological database and resource used by a diverse community of teachers, students, and researchers in academia and industry worldwide. This history is described in an article published in an issue of Acta Crystallographica that commemorates various milestones in the crystallographic community:

Helen M. Berman (2008) The Protein Data Bank: a historical perspective Acta Cryst. A64: 88-95. doi: 10.1107/S0108767307035623

A paper describing the work done as part of the wwPDB Remediation Project, including the standardization of IUPAC nomenclature for chemical components, an update of sequence database references and taxonomies, and improvements in the representations of viruses, has been published in Nucleic Acids Research's 2008 Database Issue.

K. Henrick, Z. Feng, W. F. Bluhm, D. Dimitropoulos, J. F. Doreleijers, S. Dutta, J. L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C. L. Lawson, J. L. Markley, H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E. L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin, H. M. Berman (2008) Remediation of the Protein Data Bank archive Nucleic Acids Research 36: D426-D433. doi: 10.1093/nar/gkm937

The data from the Remediation Project are available through the FTP archive and wwPDB member sites. Detailed documentation about the Remediation Project is available at

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