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

Winter 2008
Number 36

Home | Newsletter Archive | PDF Version | Text-only Version

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


Web Survey: RCSB PDB Educational Resources

Do you use the Molecule of the Month? Teach classes? Use the RCSB PDB when working with students? Then we want to hear from you!

The RCSB PDB is looking for feedback about the educational resources available from our
website, and in particular, the types of educational activities and resources that are of interest to our users.

We have created a short online survey at ZPP48MNM that should only take a few minutes to answer.

We greatly appreciate your participation in this survey. As a token of appreciation, we will send temporary tattoos of tRNA to survey respondents who send their postal address to The survey will be closed at the end of this quarter.

A temporary tattoo of 4tna can be yours!

RCSB PDB Poster Prize Awarded at AsCA

Thanks to everyone who participated in the RCSB PDB Poster Prize competition at the 8th Conference of the Asian Crystallographic Association (AsCA) that took place November 4 through 7, 2007 in Taipei, Taiwan.

The RCSB PDB Poster Prize is awarded to the best student poster related to macromolecular crystallography. At AsCA, the judges interviewed the finalists for the prize, and considered the engagement of the student in the work and their understanding of it; the clarity of the presentation in terms of the hypothesis being tested; the appropriateness of the approach; and the justification of the conclusions drawn based on the data presented.

The award went to Serah Kimani for the poster "Why do nitrilases need to form helices to be active?" (Trevor Sewell, Serah Kimani (University of Cape Town), and Muhammed Sayed (University of the Western Cape, South Africa)). Serah will receive a copy of International Tables Volume B - Reciprocal space and a subscription to Science.

AsCA poster prize winner Serah Kimani

Judges: Mitchell Guss (University of Sydney), Sine Larsen (European Synchrotron Radiation Facility), and Mike Lawrence (Walter and Eliza Hall Institute of Medical Research).
Poster Prize Chairman: Jill Trewhella (University of Sydney)

Special thanks to the AsCA organizers and the Program Committee Chairman Se Won Suh for their assistance with organizing the prize. Congratulations to all of the 2007 RCSB PDB Poster Prize award winners.

Flyers Available in Print and Online

The News & Publications web page, accessible from, offers links to various RCSB PDB publications, including newsletters and annual reports. Educational brochures describe different educational features, including the Sea of Genes exhibit in the Birch Aquarium at Scripps Research Institute that explored proteins related to underwater creatures.

Other brochures help users explore the RCSB PDB. 5 Easy Steps for Structure Deposition describes the tools that facilitate NMR and X-ray crystal structure deposition and validation for use by depositors.

A General Information trifold provides an overview of the RCSB PDB project, and includes information about data deposition, data query and reporting, Molecule of the Month, structural genomics, wwPDB, and outreach and education resources.

All of these materials can be downloaded from the RCSB PDB site. To receive printed copies of any flyers, please send your postal address and request to Multiple copies may be requested.

2008 Calendar Now Available

A calendar showcasing PDB structures is now available online. Printed copies are also available via



RCSB PDB Paper Cited More Than 5,000 Times

According to Essential Science Indicators 1, the RCSB PDB primary reference is ranked #4 in the top cited Biology and Biochemistry papers of the past ten years. "The Protein Data Bank,"2 published in the 2000 Database Issue of Nucleic Acids Research, has been cited more than 5,000 times.

In-cites magazine featured this paper in an interview with RCSB PDB Director Helen M. Berman at

  1. Essential Science IndicatorsSM:
  2. The Protein Data Bank. (2000) Nucleic Acids Research, 28, pp. 235-242.


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