DATA DEPOSITION AND PROCESSING

2005 Deposition Statistics

In 2005, 6491 experimentally-determined structures were deposited to the PDB archive – a 21% increase over 2004's 5356 depositions.

The entries were processed by wwPDB teams at RCSB-Rutgers, MSD-EBI, and PDBj. Of the structures deposited in 2005, 69.2% were deposited with a release status of "hold until publication"; 17.0% were released as soon as annotation of the entry was complete; and 13.8% were held until a particular date.

81.1% of these entries were determined by X-ray crystallographic methods; 15.3% were determined by NMR methods. 80.7% of these depositions were deposited with experimental data.




PDB Focus: Restarting ADIT depositions

A structure can be deposited in more than one Internet session by using ADIT's "Session Restart ID" feature. This identifier appears in red in the center of the browser window when ADIT's "deposit" step is first started. It is also seen in the title of the browser throughout the deposition session.

The case-sensitive restart ID should be entered in the space provided on the ADIT home page to return to the undeposited entry. Any data entered in a category are stored every time the user selects the SAVE button. 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.

ADIT is available at the RCSB PDB and PDBj. A tutorial guide to using ADIT is available in English and Japanese. Example "in progress" deposition sessions are available to practice learning how to use ADIT at rcsb-deposit-demo-1.rutgers.edu.


The restart ID can be used to work on a deposition at a later time.




PDB Focus: First Time Depositors...

There are a few steps a depositor can take to make the process of depositing a structure to the PDB quick, easy, and accurate! This is an iterative process - if you encounter problems at a particular step, please make the correction(s) and go through the steps again. These resources are all linked from deposit.rcsb.org.

  1. Use the pdb_extract Program Suite to extract information needed for deposition from output files produced by many structure determination applications.
  2. Check your structure with the Validation Suite and Server to ensure that the data being deposited is accurate and reflects what you intend to submit.
  3. Run BLAST (at NCBI) to compare your sequence to sequence database references. Any necessary corrections can then be made to your sequence and coordinates.
  4. Use Ligand Depot to find the proper codes for existing ligands, to link to other entries with a particular ligand, and to search for substructures.
  5. Deposit your structure using ADIT, using its editor to add any missing information to the deposition.

For a detailed packet of information about first-time deposition, including reprints about validation and Ligand Depot, please send your postal address to info@rcsb.org with the subject line "first time depositor packet"




PDB Focus: Ligand Depot—a Small Molecule Information Resource

Ligand Depot is a data warehouse that integrates databases, services, tools, and methods related to small molecules bound to macromolecules.

An important tool to use when depositing PDB structures, this resource can be used to find codes for existing ligands, to link to other entries with a particular ligand, and to search for substructures.

If a ligand related to a deposition is not in Ligand Depot, please email the chemical diagram, name, and formula to deposit@rcsb.rutgers.edu.

Ligand Depot: a data warehouse for ligands bound to macromolecules Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, and John Westbrook. (2004) Bioinformatics 20, pp. 2153-2155.