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

Fall 2008
Number 39

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Message from the RCSB PDB
Data Deposition
Announcement: Comprehensive Format Guide Version 3.2
Ligand Expo: A Resource for Depositing Structuress
PDB Focus: What is the smallest polymer structure that can be deposited to the PDB?
ADIT Focus: Restarting Deposit Sessions
Deposition Statistics
Data Query, Reporting and Access
Exploring Structures Through PubMed Abstracts
Website Statistics
Outreach and Education
Meetings and Presentations
DOIs for PDB Structures and the Molecule of the Month
RCSB PDB Poster Prizes
wwPDB Paper: Representation of viruses in the Remediated PDB
Education Corner
Molecular Visualization in your Pocket by Dr. Brad Larson, Sunset Lake Software
PDB Community Focus
Paul D. Adams, Ph.D., Lawrence Berkeley Laboratory

Outreach and Education

RCSB PDB Meetings and Presentations

The RCSB PDB and the wwPDB have been participating in several meetings:

  • At the 22nd Annual Symposium of The Protein Society (July 19-23; San Diego, CA), Peter Rose presented the poster "Effective Mining of the Protein Data Bank" which explored the many different search functions available from

  • Many PDB users stopped by the RCSB PDBs exhibit booth at the 16th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB; July 19-23; Toronto, Canada), the official conference of the International Society for Computational Biology (ISCB). Associate Director Phil Bourne was involved in many presentations and discussions, and delivered a 3DSig Keynote Lecture at the Structural Bioinformatics and Computational Biophysics satellite meeting.

  • At the XXI Congress & General Assembly of the International Union of Crystallography (IUCr; August 23 31; Osaka, Japan) wwPDB members from around the globe hosted a joint exhibition stand for demonstrations, met with users, and participated in a variety of sessions and commission meetings.

    Also at the IUCr meeting, RCSB PDB Director Helen M. Berman presented a keynote lecture entitled What the Protein Data Bank tells us about the past, present, and future of structural biology, and John Westbrook presented Data Quality in the PDB Archive. Professor Berman also participated in a Question and Answer session at the Commission on Biological Macromolecules.

The wwPDB exhibit stand at the IUCr meeting: 1. Helen Berman and Haruki Nakamura (PDBj) 2. James Watson (EMBL); 3. John Westbrook at the wwPDB booth, which highlighted resources at all member sites; 3. IUCr attendees;
  • As part of the International Structural Genomics Organization's Conference on Structural Genomics (Sept. 20-24; Oxford, UK), RCSB PDB Director Helen Berman described the PSI Structural Genomics Knowledgebase.

  • At the EMBO 08 Practical Course on Computational Aspects of the Protein Target Selection, Protein Production Management and Structure Analysis Pipeline (Sept. 22-26; Hinxton, UK), Helen Berman and John Westbrook (RCSB PDB), Haruki Nakamura (PDBj), and Kim Henrick, Dimitris Dimitropoulos, Eugene Krissinel, and Tom Oldfield (PDBe) led tutorial sessions about various resources and tools from wwPDB sites.

  • At the European Conference in Computational Biology (ECCB 08; Sept. 22-26; Sardinia, Italy), Martha Quesada and Andreas Prlic (RCSB PDB) gave an overview of the multifaceted wwPDB collaboration and demonstrated features found at the RCSB PDB, PDBe, PDBj, and BMRB websites.

  • Upcoming RCSB PDB events include the New Jersey Science Convention for science teachers (October 14-15; Somerset, NJ), eCheminfo Community of Practice Meeting on Advances in Drug Discovery and Development (October 13-17; Philadelphia, PA), the meeting of the Association of Science and Technology Centers (October 18-21; Philadelphia, PA) and the Pittsburgh Diffraction Conference (October 30-November 1; Pittsburgh, PA).

DOIs for PDB Structures and the Molecule of the Month

Image of ribonuclease A from the September 2008 RCSB PDB Molecule of the Month feature (10.2210/rcsb_pdb/mom_2008_9)
by David Goodsell

PDB structures can be cited using their PDB ID and the related published citation. Structures may also be referenced using their Digital Object Identifier (DOI). These DOIs are formatted as 10.2210/pdbXXXX/pdb, where XXXX is the PDB ID. For example, the DOI for entry 4hhb is "10.2210/pdb4hhb/pdb".

DOIs can be used in a URL ( or entered in a DOI resolver (such as to automatically link to file pdb4hhb.ent.gz on the main PDB FTP archive. DOIs are also available for RCSB PDB Molecule of the Month features in the format: 10.2210/rcsb_pdb/mom_YYYY_MM (where YYYY is the year and MM the number of the month, using one or two digits). For example, the DOI for the May 2003 feature on hemoglobin by Shuchismita Dutta and David S. Goodsell is "10.2210/rcsb_pdb/mom_2003_5". These features are referenced with the DOI and the author/s of the article.

A page describing policies & references for using and citing PDB data and RCSB PDB resources is available at

RCSB PDB Poster Prizes

The RCSB PDB Poster Prize for best student poster related to structure and function prediction at the ISCBs ISMB meeting went to Dariya Glazer for Clustering Across Space and Time (Dariya Glazer, Randy Radmer, Russ Altman; Stanford University).

Chaille T. Webb
At the IUCr meeting, the judges found that the best student poster related to macromolecular crystallography was "Structural insights into the mitochondrial import complex, TIM9.10" by Chaille T. Webb,1,2 Michael Baker,1 Michael T. Ryan,1 Peter M. Colman,1 and Jacqueline M. Gulbis1(1The Walter and Eliza Hall Institute of Medical Research and 2The University of Melbourne, Australia)

The winners will receive a subscription to Science and a related reference book.

Special thanks to our judges and the conference organizers.


wwPDB Paper: Representation of viruses in the Remediated PDB

The article was also highlighted on the journal cover.
The 2007 release of remediated data improved the representation of deposited and experimental coordinate frames, symmetry, and frame transformations in the archive.

A paper describing the scheme used by the wwPDB to represent viruses and other biological assemblies with regular noncrystallographic symmetry has been published:

C.L. Lawson, S. Dutta, J.D. Westbrook, K. Henrick and H. M. Berman (2008) Representation of viruses in the remediated PDB archive Acta Cryst. D64: 874-882


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