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

Fall 2009
Number 43

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Message from the RCSB PDB
Data Deposition
SF-Tool: A Tool for Crystallographic Experimental Data Validation
Meeting with Depositors at the ACA Meeting
Deposition Statistics
Structural Genomics News
Data Query, Reporting and Access
Improved Navigation of the RCSB PDB Website
Sequence Similarity Views of PDB Structures
New Tool For Exploring Sequence and Structure Alignments
Beta Release of Redesigned BioSync
wwPDB FTP Advisory Notice
Outreach and Education
Poster Prizes Awarded at ACA and ISMB
Recent and Upcoming Meetings and Presentations
Turn Your Computer into a PDB Structure Kiosk
Education Corner
Gary M. Battle, Ph.D.: Symposium on the Applications of Small-molecule Crystal Structure Information in Chemical Education
PDB Community Focus
Roland L. Dunbrack, Jr., Ph.D., Fox Chase Cancer Center

Outreach and Education

Recent and Upcoming Meetings and Presentations

ACA Poster Prize Winner Magdalena Korczynska with Victor Young and ACA President Dr. Robert Von Dreele.
Magdalena Korczynska was awarded the RCSB PDB Poster Prize for best student poster related to macromolecular crystallography at the ACA Annual Meeting for Structural Insight into Homoserine Transacetylase from Haemophilus influenzae (Magdalena Korczynska,a I. Ahmad Mirza,a and Albert M. Berghuis;a,b
Departments of Biochemistry and bMicrobiology & Immunology, McGill University, Montreal, QC, Canada).

Many thanks to the judges: Joe Ng (The University of Alabama in Huntsville), John Rose (University of Georgia), and Emil Pai (University of Toronto).

Christoph Malisi
The award for the best student poster in the category structure function and prediction at the Joint 17th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB) and the 8th European Conference on Computational Biology (ECCB; June 27-July 2; Stockholm, Sweden) went to Christoph Malisi for Automated Scaffold Selection for Enzyme Design (Christoph Malisi,a,b Oliver Kohlbacher,b and Birte Höcker;a
Max Planck Institute for Developmental Biology, Protein Design Group, Tübingen, Germany; bDivision for Simulation of Biological Systems, Center for Bioinformatics, Eberhard-Karls-Universität Tübingen, Germany).

Many thanks to the judges: Marco Punta (Committee Chair, Columbia University), Yana Bromberg (Columbia University), Stefano Lise (University College London), Silvio Tosatto (Universita' di Padova, Italy), Maria Valentini (CRS4, Italy), Curtis Huttenhower (Harvard University), and Lars Arvestad (KTH Royal Institute of Technology, Sweden). Thanks also to the full reviewing committee and to the International Society for Computational Biology.

The winners will receive an educational book and a subscription to Science magazine.

Recent and Upcoming Meetings and Presentations

The RCSB PDB exhibited along side the PSI SG KB at the 23rd Annual Symposium of The Protein Society (July 25-29, Boston, MA). Lihua Tan presented the poster A Lot More Than Coordinates: A Short Tour of a PDB File, which highlighted all of the rich information available in a PDB file other than the X, Y, Z coordinates.

Demonstrations of new RCSB PDB features were given at the Joint 17th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB) and the 8th European Conference on Computational Biology (ECCB) (June 27-July 2; Stockholm, Sweden). At the ISMB satellite Bioinformatics Open Source Conference (BOSC), the RCSB PDB's Andreas Prlic presented BioJava 2009: an Open-Source Framework for Bioinformatics, and at the BioLink Special Interest Group Session on the Future of Scientific Publishing, Phil Bourne discussed OpenID vs. ResearcherID.

At the Essentials for Educating Biochemistry and Molecular Biology Undergraduates Symposium (August 5-8; Colorado Springs, CO) sponsored by the American Society for Biochemistry and Molecular Biology, Shuchismita Dutta ran a workshop entitled Molecular Visualization and Protein Databases (IIA): Tools, Rules and Stories: A Protein Data Bank Workshop Series.

The RCSB PDB will exhibit at the American Society for Cell Biology meeting at the end of 2009 (December 5-9; San Diego, CA) and at the Biophysical Society meeting at the beginning of 2010.

Turn Your Computer into a PDB Structure Kiosk

Highlight structures from your lab, institution, or class with the Molecules in Motion Kiosk Viewer. Using a list of PDB IDs, this full-screen animation program will display any PDB structure from different angles and perspectives. It also focuses on any chemical components within the structure.

The Java viewer can be downloaded or launched from the Educational Resources page.

The Molecules in Motion Kiosk Viewer on display at the Busch Campus Center at Rutgers, The State University of New Jersey.

High School Teams to Build 3D Protein Models

The protein modeling event will be held at more than 20 Science Olympiad tournaments held across the country in 2010. The theme for the competitions will be influenza, with teams building models of hemagglutinin and neuraminidase.

The RCSB PDB supervises and judges the competition in New Jersey ( and will be posting tips and news at

The event was developed by the Center for BioMolecular Modeling. For more information, please see

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