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

Summer 2008 Number 38

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Data Deposition
SF-Tool: A Tool for Crystallographic Experimental Data Validation
Ligand Expo: A Small Molecule Resource
Workshop on Next Generation Validation Tools for the wwPDB
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
Secondary Structure Information
RCSB PDB Usage Statistics
Outreach and Education
RCSB PDB Meetings and Presentations
RCSB PDB Poster Prize Awarded at ACA Meeting
Princeton High School Students Win New Jersey Science Olympiad Protein Modeling State Finals
Congratulations to National Tournament Champions
Papers Published
Structural Displays
Education Corner
Biochemistry and Molecular Biology Education, a Journal for University, College, and High School Educators by Judith G. Voet and Donald H. Voet
PDB Community Focus
John Norvell, Ph.D., National Institute of General Medical Sciences

RCSB PDB Meetings and Presentations

The RCSB PDB has been exhibiting at several meetings, including:

  • The American Crystallographic Association?s Annual Meeting (May 31-June 5, 2008; Knoxville, TN)
  • The Experimental Biology Annual Meeting, which is attended by the members of the American Society for Biochemistry and Molecular Biology (April 5-9, 2008; San Diego, CA)

RCSB PDB members routinely give oral presentations at meetings. Here are recent highlights:

  • John Westbrook described the process of "Automating PDB Deposition" at the Cold Spring Harbor Laboratory?s (CSHL) X-ray Crystallography Course X-ray Methods in Structural Biology (April 29-May 15, 2008). This year?s class was held at the Chinese Academy of Sciences in Beijing, China and chaired by Zihe Rao. For a description of this class, please see the Winter 2007 Education Corner article by one of the organizers, Gary Gilliland.

The lecturers and students of the CSHL X-ray Crystallography Course

  • As part of the Sigma Xi Distinguished Lecturers series for 2008-2009, Director Helen Berman discussed ?How the History of the Protein Data Bank Informs the Future of Biology? at Ramapo College (NJ), SUNY College at Old Westbury, and Indiana University of Pennsylvania. She also spoke at Montana State University as part of the Women In Bioinformatics seminar series.
  • Peter Rose led an RCSB PDB workshop and a demonstration at From Molecules to Medicine: Integrating Crystallography in Drug Discovery (May 29 - June 8, 2008; Erice, Italy)

RCSB PDB Poster Prize Awarded at ACA Meeting

Wei Yong, RCSB PDB Poster Prize winner at ACA

The RCSB PDB Poster Prize for best student poster related to macromolecular crystallography at the American Crystallographic Association's Annual Meeting (May 31 - June 5, 2008; Knoxville, TN) went to Wei Yong for "X-ray crystallographic studies of pig sarcosine dehydrogenase" (Wei Yong, Ila Misra, Jung-Ja Kim, Medical College of Wisconsin).

Yong will receive a subscription to Science and an International Tables of Crystallography volume of his choosing.

Thanks to everyone who participated, especially our judges: Robert Rose (Chair; North Carolina State University); Gloria E.O. Borgstahl (Eppley Institute for Cancer Research and Allied Diseases); Antonella Longo (North Carolina State University); Robert McKenna (University of Florida); and Joseph E. Wedekind (University of Rochester).

Other RCSB PDB Poster Prizes will be awarded this year at the 16th Annual International Conference on Intelligent Systems for Molecular Biology (July 19-23, 2007; Toronto, Canada) and the Congress and General Assembly of the International Union of Crystallography (August 23-31, 2008; Osaka, Japan).

Princeton High School Students Win New Jersey Science Olympiad Protein Modeling State Finals

The team from Princeton High School that came in first place at the 2007 Protein Modeling event at the Science Olympiad State Finals in New Jersey held on to their title at this year?s competition.

Left: Princeton High School students and their model of calmodulin.
From left to right: Ola Hadaya, Sarah Goodman, and Asya Kosygina.
Right: Teams built a portion of the calmodulin structure using online resources during the event.

Teams from all over the Garden State presented their hand-built 3D models of a calmodulin protein, along with an abstract, to be judged by staff from the RCSB PDB at the March 11 meet. At the competition, teams built a model of a selected region of the structure using Jmol and took a written exam about the structure.

Teams used the RCSB PDB Molecule of the Month and other resources to help prepare for this event.

Following Princeton High School (First Place) came Livingston High School (Second), and West Windsor-Plainsboro High School North (Third).

Congratulations to all participating teams?there were many great models, abstracts, and responses to the written exam. Pictures of the event and rubrics used in judging are available at Questions about the NJ Science Olympiad Protein Modeling trial event should be sent to

Special thanks to our judges from the RCSB PDB (Andrei Kouranov, Chenghua Shao, Irina Persikova, Jasmine Young, Jing Zhou, and Christine Zardecki (Event Supervisor)), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.

The models were carefully judged by RCSB PDB staff.

Congratulations to National Tournament Champions

At the Science Olympiad National Tournament held on May 30-31, 2008 at The George Washington University, New Jersey?s West Windsor-Plainsboro High School North won first place at the protein modeling event.

Aleesha Shaik, Ilya Podkopaev, and Brian Lee

Papers Published

? wwPDB deposition tools, methods (including validation), and policies are discussed in:
Data deposition and annotation at the Worldwide Protein Data Bank. Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, Helen M. Berman (2008) in Methods in Molecular Biology, vol. 426: Structural Proteomics: High-Throughput Methods (Bostjan Kobe, Mitchell Guss, Thomas Huber, eds.), pp. 81-101.

? Issues relating to NMR depositions are outlined in:
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. John L. Markley, Eldon L. Ulrich, Helen M. Berman, Kim Henrick, Haruki Nakamura, and Hideo Akutsu (2008) J Biomol NMR 40(3): 153-155.

? Resources and efforts to ensure that PDB data are used by scientists, students, and teachers inside and outside of the structural biology community are described in:
Interesting structures: Education and outreach at the RCSB Protein Data Bank. Christine Zardecki (2008) PLoS Biology 6:e117. doi: 10.1371/journal.pbio.0060117

Structural Displays

Monitors that show rotating proteins and nucleic acids are on display on the campuses of UCSD and Rutgers. The set of entries highlighted includes structures solved on campus and structures related to human health. The program ?floats? each structure across the screen before moving on to the next.

PDB entries related to Nobel Prizes and structures that have been solved at the university are on display at the Busch Campus Center at Rutgers.

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