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

Spring 2009
Number 41

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Message from the RCSB PDB
Data Deposition
PDB Archive Version 3.15 Released
Papers Published
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
New Feature: Receive Email Alerts When New Structures Match Your Queries with MyPDB
Time-stamped Copies of PDB Archive Available via FTP
Outreach and Education
New Jersey Science Olympiad: Protein Modeling
Education Corner
Gavin Whittaker, Ph.D.,
Molecular Models: Tangible Representations of the Abstract
PDB Community Focus
GaŽl McGill, Ph.D., and Graham Johnson, Molecular Animators


Website Statistics

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New Feature: Receive Email Alerts When New Structures Match Your Queries with MyPDB

MyPDB is a new feature that regularly sends out emails when structures that match customized queries are released. The matching structures can be accessed directly from the email alerts. Users can also log in to MyPDB to run stored searches at any time.

To sign up for MyPDB, users should register using the link at the top right of the RCSB PDB header.

MyPDB registration (circled), login, and logoff links are all found in the top right corner of the
RCSB PDB website.

Following registration, an activation link is sent in a confirmation email. After activating the MyPDB account, users can log in at the top of the page. Next, users can review currently saved queries and update MyPDB account information. This page can also be accessed by clicking on the user name at the top of the page.

Saved queries can include combinations of searches by keyword, sequence, ligand, and Advanced Search. To store a query in a profile, users should query the RCSB PDB website, such as an Advanced Search for structures with Enzyme Commission Number 2.7.11. After evaluating the query, the Queries tab in the left menu will temporarily store the search. Selecting Save Query to MyPDB option from this tab will store the search in MyPDB.

Queries performed at the RCSB PDB website can be saved in MyPDB for future use.
Email notifications can be sent when structures matching saved queries are released.

From the MyPDB page, users can click on the query name and query description to personalize them.

Query names, descriptions and notification schedule can all be customized in My PDB.

By default, the email notification is turned on. The Next Scheduled Run indicates when the query is next run. Email alerts can be set to run weekly (Tuesday afternoon Pacific Time) or monthly (on the first Tuesday).

The email includes the customized query name and a list of matching PDB IDs that have been recently released. Clicking on the query name takes users to the results set at the RCSB PDB website; the results can then be further refined, exported, or further explored. Each PDB ID links to the entry’s Structure Summary page.

Questions about this new feature can be sent to

Time-stamped Copies of PDB Archive Available via FTP

Snapshots of the PDB archive ( as of January 5, 2009 and March 16, 2009 have been added to Time-stamped snapshots of the PDB have been archived since 2004. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

The script at may be used to make a local copy of a snapshot or sections of a snapshot. The directories include the experimentally-determined coordinate files that were current at time the snapshote was created. Coordinate data are available in PDB, mmCIF, and XML formats. The date and time stamp of each file indicates the last time the file was modified.

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