pdb_extract Now Supports NMR Depositions

The program pdb_extract¹, which has been simplifying the deposition of crystal structures, can now be used for NMR depositions. The latest version supports NMR-related information from the applications X-Plor/CNS/CNX, CYANA, and DYANA. Other enhancements made to the pdb_extract suite are detailed in the Version Release Notes available from the pdb_extract website.

pdb_extract minimizes errors and saves time during the deposition process since fewer data items have to be manually entered.

The program extracts key details from the output files produced by many X-ray crystallographic and NMR applications for use in the deposition process. The program merges these data into macromolecular Crystallographic Information File (mmCIF) data files that can be used with ADIT to perform validation and to add any additional information for PDB deposition.

pdb_extract can be used via web interface or downloadable workstation from pdb-extract.rcsb.org.

¹Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. (2004) Acta Cryst. D60, pp. 1833-1839.

PDB Archive Focus: Worldwide Data Annotation

Data from X-ray crystallographic, NMR, and cryo-electron microscopic experiments are deposited to the PDB archive by scientists from all over the world.

PDB data are processed by an international effort involving members of the wwPDB – the RCSB PDB, the Macromolecular Structure Database at the EMBL's European Bioinformatics Institute, and Protein Data Bank Japan. wwPDB annotators work with these data to make sure they are represented in the PDB archive in the best way possible. They run a series of checks, make corrections, and correspond with the depositors in an effort to make the data public as quickly and accurately as possible.

Statistics about the number of structures deposited, processed, and released by the wwPDB are available at http://www.wwpdb.org/stats.html

2006 Deposition Statistics

In the first half of 2006, 3547 structures were deposited to the PDB archive.

The entries were processed by the wwPDB teams at RCSB PDB, MSD-EBI, and PDBj. Of the structures deposited, 70% were deposited with a release status of "hold until publication"; 17% were released as soon as annotation of the entry was complete; and 13% were held until a particular date.

81% of these entries were determined by X-ray crystallographic methods; 15% were determined by NMR methods; and 82% of all of these depositions were deposited with experimental data.