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

Summer 2009
Number 42

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Message from the RCSB PDB
Data Deposition
5 Easy Steps for Structure Deposition
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Deposition Statistics
Data Query, Reporting and Access
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Literature View: Looking at Structures in PubMedCentral
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Ligand Expo: Searching and Browsing Features
Outreach and Education
Recent and Upcoming Meetings and Presentations
Congratulations to National Tournament Champions
wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe
Looking at Structures: A Resource for Learning About PDB Data
Education Corner
Community Outreach
PDB Community Focus
Gregory Warren, OpenEye Scientific Software, Inc.

Outreach and Education

Recent and Upcoming Meetings and Presentations

Experimental Biology 2009

The RCSB PDB has recently exhibited with the PSI Structural Genomics Knowledgebase at the:

  • • 2009 Experimental Biology meeting (April 18-22) in New Orleans, Louisiana.
  • • Joint 17th Annual International Conference for Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology (June 27-July 2; Stockholm, Sweden). RCSB PDB members also gave presentations at satellite and special interest group sessions.

Exhibition booths and posters will also be presented at the 23rd Annual Symposium of The Protein Society (July 25-29; Boston, MA) and the 2009 Annual Meeting of the American Crystallographic Association (July 25-30; Toronto, Canada).

At the Essentials for Educating Biochemistry and Molecular Biology Undergraduates Symposium sponsored by the American Society for Biochemistry and Molecular Biology (August 5-8; Colorado Springs, CO), the RCSB PDB's Shuchismita Dutta and Rachel Kramer will run a workshop entitled “Molecular Visualization and Protein Databases (IIA): Tools, Rules and Stories: A Protein Data Bank Workshop Series.” For more information about this workshop, please see

Congratulations to National Tournament Champions

Congratulations to Nikita Singh and Ankita Gore, who received scholarships to the Milwaukee School of Engineering for winning this event.

At the Science Olympiad National Tournament held May 15-16, 2009 at Augusta State University in Augusta, Georgia, New Jersey’s West Windsor-Plainsboro High School North won first place at the protein modeling event.

In 2010, the protein modeling trial event will take place at all of the Science Olympiad competitions held in the United States. For more information about this event, see the Center for BioMolecular Modeling’s site at or the RCSB PDB protein modeling site at




wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe

Kim Henrick and Gerard Kleywegt

Starting July 1, 2009, Gerard Kleywegt will lead the Protein Data Bank Europe (PDBe) project at the European Bioinformatics Institute (Hinxton, UK). During the last 17 years he has been working in Uppsala, Sweden, a center of excellence for biomolecular crystallography, and has developed many tools that are widely used by structural biologists worldwide. He has an extensive publication record and has served on the PDBe Scientific Advisory Board for the last few years. He has also been one of the European representatives on the wwPDB advisory committee. He has a very strong international reputation and is well respected in the structural biology community.

Gerard will be replacing Kim Henrick, who has been the team leader of the PDBe since 2001. During his tenure at the EBI, Kim has made enormous contributions to the PDBe by establishing and leading a strong team that has developed a wide variety of services. Kim was a strong advocate for the formation of the wwPDB in 2003. He has played a key role in developing the standards for representing all the data in the archive, from small molecules to very large biological assemblies, and in leading the remediation efforts. Kim's deep knowledge of the PDB, his critical eye, and sharp wit will be greatly missed by the wwPDB.

The members of the wwPDB look forward to working closely with Gerard and wish Kim all the best in the next chapter of his career.

Looking at Structures: A Resource for Learning About PDB Data

Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file? These questions and many others are explored in the RCSB PDB's new Looking at Structures.

Using text, images, and interactive Jmols, Looking at Structures intends to help researchers and educators get the most out of the PDB archive.

Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring the archive.

A Table of Contents appears on the right side of every page so at any time users can access the individual pages: Biological Units, Dealing with Coordinates, Methods for Determining Structure, Missing Coordinates and Biological Units, Molecular Graphics Programs, Resolution, and R-value and R-free. The addition of future topics is planned.

Looking at Structures is available from the General Education section of the left-hand menu.

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