Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Winter 2011
Number 48
 
NEWSLETTER
  Contents  
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Message from the RCSB PDB
Data Deposition
Deposition Statistics
Deposition Session Restart IDs
Data Query, Reporting and Access
2010 Website Statistics
Latest Website Release
Binding Affinity Data Integration
Creating Tabular Reports
New Data Distribution Summaries
New Ligand Summaries
Web Services
Outreach and Education
Molecules of 2010
Responses Needed: Quick survey on the educational uses of molecular visualization
Annual Report Published
Poster Prize Awarded at AsCA
Recent Meetings and Events
25th Annual Meeting on HIV/AIDS-related Structural Biology
Education Corner
Jaime Prilusky, Ph.D.
Proteopedia: An online, collaborative 3D-encyclopedia of proteins & other molecules
RCSB PDB PARTNERS, MANAGEMENT, AND STATEMENT OF SUPPORT
 
     

DATA DEPOSITION AND ANNOTATION

Deposition Statistics

´╗┐In the fourth quarter of 2010, 2123 experimentally-determined structures were deposited to the PDB archive for a total of 8865 entries deposited in the year.

Of the structures deposited in 2010, 77.0% were deposited with a release status of "hold until publication"; 19.2% were released as soon as annotation of the entry was complete; and 3.8% were held until a particular date.

92.3% of these entries were determined by X-ray crystallographic methods; 6.8% were determined by NMR methods. 7,971 structures were released in the PDB archive in 2010. They account for 11% of the current total holdings of 70,231 entries.

Number of entries deposited per year (2001 - 2010)

 



Deposited entries are processed and annotated by the wwPDB before release into the archive.

Location of depositor for entries deposited in the years 2001 and 2010

 



Experimental type of entries deposited in the years 2001 and 2010

 



Release status for entries deposited in the years 2001 - 2010

 



Depending upon the hold status selected by the depositor, data release occurs when a depositor gives approval to the finalized entry (REL), the hold date has expired (HOLD), or the journal article describing the structure has been published (HPUB). A one-year limit on HOLD or HPUB was instituted in 2003.


Deposition Session Restart IDs

Need more time to deposit an entry? ADIT 2.0 can email a restart ID to continue a deposition session at a later time.

Depositing a PDB entry can take place over a period of time using ADIT's "Session Restart ID" feature. Each deposition session has a single ID that can be emailed to the depositor and used to restart the session at a later date.

After initially uploading files, ADIT 2.0 runs checks for data format, validation, and sequence. On each of these pages, select "Click here to e-mail the session restart ID" to send an email containing the restart ID.

This identifier also appears in the title and the initial center panel of the ADIT editor window.

The unique case-sensitive restart ID, a combination of the date, time, computer IP, and session number, is generated automatically. It should be entered in the space provided on the ADIT home page to return to the deposition session. All entered data associated with a particular entry can be accessed using the restart ID until the "DEPOSIT NOW" button is selected, for up to six months after the session has been last updated.

 
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