ENHANCED DESIGN AND CONTENT OF RCSB PDB DATA DEPOSITION SERVICES
The RCSB PDB has further developed the web pages that describe data
deposition. The main page at deposit.pdb.org links to the software and
resources that can be used for preparing, checking, validating and
depositing structural data to the PDB. It also provides individual
guidelines for preparing structures determined by X-ray
crystallography, NMR, or electron microscopy.
Tutorials are available for ADIT, pdb_extract, the Validation Suite,
and Ligand Depot. A guide for converting a structure factor file into
mmCIF format is also available.
A FAQ is provided to answer questions on a variety of subjects --
deposition, update, and release policies (such as "How do I replace
coordinates? How do I deposit a new chemical component/ligand?"),
ADIT ("How can I base a new deposition on an older one?"), Validation
("I keep getting an error message -- what could be wrong?"), and
pdb_extract ("What does pdb_extract do?").
It is recommended that all depositors review this page and its
associated links in order to make their data deposition process
quicker, easier, and more complete and accurate. We welcome your
comments on these pages at email@example.com.
PDB FOCUS: WORLDWIDE DATA ANNOTATION
PDB data are processed by an international effort involving members of
the wwPDB -- RCSB, MSD-EBI, and PDBj.
|RCSB annotator Suzanne Richman on a visit to PDBj, where she processed data for two months. From left to right: Shinobu Saeki, Yumiko Kengaku, Reiko Igarashi, Suzanne Richman, Yasuyo Morita, and Takashi Kosada.
Structures deposited using ADIT are annotated by staff from the RCSB
(at Rutgers University in New Jersey and remotely at the Academy of
Sciences of the Czech Republic) and PDBj in Osaka, Japan.
AutoDep depositions are processed by the MSD-EBI team in the United
PDB DEPOSITION STATISTICS
In 2004, 5356 experimentally-determined structures were deposited to
the PDB archive -- a 14 1/2% increase over 2003's 4677 depositions.
The entries were processed by teams at RCSB-Rutgers, MSD-EBI, and
PDBj. Of the structures deposited in 2004, 76% were deposited with a
release status of "hold until publication"; 14% were released as soon
as annotation of the entry was complete; and 10% were held until a
particular date. 83% of these entries were determined by X-ray
crystallographic methods; 14% were determined by NMR methods. 78% of
these depositions were deposited with experimental data. 58% of these
depositions released the sequence in advance of the structure's
PDB FOCUS: LIGAND DEPOT--A SMALL MOLECULE INFORMATION RESOURCE
Ligand Depot (ligand-depot.rutgers.edu) 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
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