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

Spring 2010
Number 45

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Message from the RCSB PDB
Data Deposition
Deposition Statistics
wwPDB News: Changes to the wwPDB Policy for Depositing Polypeptide Structures
wwPDB News: Initial Release REVDAT Dates
Data Query, Reporting and Access
Website Statistics
Improved Ligand Searching
Comparison Tool for Exploring Sequence and Structure Alignments
Advanced Search: Sequence Motif
Time-stamped Copies of PDB Archive Available via FTP
Outreach and Education
Online Narrated Tutorial Demonstrates How to Use the RCSB PDB
Poster Download: How Do Drugs Work?
NJ Science Olympiad Protein Modeling Results
Recent and Upcoming Meetings and Events
Education Corner
Robert C. Bateman, Jr. and Paul A. Craig: A Proficiency Rubric for Biomacromolecular 3D Literacy


Deposition Statistics

In the first quarter of 2010, 2065 experimentally-determined structures were deposited to the PDB archive. The entries were processed and annotated by wwPDB teams at the RCSB PDB, PDBe, and PDBj.

Of the structures deposited, 74.7% were deposited with a release status of "hold until publication"; 22.6% were released as soon as annotation of the entry was complete; and 2.7% were held until a particular date. 92.5% of these entries were determined by X-ray crystallographic methods; 6.9% were determined by NMR methods.

During the same time period, 2027 structures were released in the PDB.

wwPDB News

Changes to the wwPDB Policy for Depositing Polypeptide Structures

The wwPDB now accepts polypeptide structure depositions of all gene products; all naturally-occurring, non-ribosomally synthesized peptides, such as antibiotics; and all peptidic repeat units of larger polymers, such as fibrous and amyloid polymers. In addition, non-naturally occurring synthetic peptides with at least 24 residues will be accepted for deposition.

Consistent with earlier policy, depositions of polynucleotide and polysaccharide structures of 4 or more residues are also accepted. For more information, see the wwPDB Policy Guide at

Initial Release REVDAT Dates

The PDB archive can be accessed at FTP sites at the RCSB PDB, PDBe, and PDBj. The update schedules for these sites have been coordinated to be simultaneous. All updates now occur at the target time of Wednesday 00:00 UTC (Coordinated Universal Time). As of March 31, 2010, the initial release date reflected in the REVDAT record mirrors the Wednesday release. The file's timestamp of the Friday before release will not be changed.

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