On January 27, 1999, the RCSB became responsible for the processing of all data received by the PDB. Brookhaven National Laboratory (BNL) will be responsible for processing the files received prior to January 27, 1999.
For now, the process of depositing data will not change. Crystal structures of proteins and all NMR structures should be deposited using either AutoDep or the PDB Deposition Form, which are available at http://www.pdb.bnl.gov/ and http://www2.ebi.ac.uk/pdb/. Crystal structures of nucleic acids should continue to be submitted directly to the Nucleic Acid Database.
After data has been deposited, it will be processed immediately by the RCSB and returned to the author. For most cases, files will be released within one week of their arrival at PDB or immediately following their release from a HOLD status. This time is based upon the extensive testing done by the RCSB over the past three months.
The files released by the RCSB will be in a fully processed and final format.
Structures deposited prior to January 27, 1999 will be processed and released according to the Layered Release Protocol previously described in the PDB Newsletter of October 1997, January 1998, and April 1998. BNL will be responsible for the completion of the processing of all files received up to that point.
In the near future, the RCSB will introduce a new Web-based tool for deposition called the AutoDep Input Tool (ADIT) at the RCSB Web site. The features of ADIT are described below. During the transition period, both AutoDep and ADIT will be available to depositors.
Questions about deposition should be sent to email@example.com.
During the transition period, which ends in October 1999, the two query engines currently available from BNL (PDBLite and 3DB Browser) will continue to be maintained by BNL and made available the BNL PDB Web sites. Additionally, new query engines will be introduced at the RCSB Web sites. Anyone using the PDBLite or 3DB Browser query engines at the BNL Web site or any of its mirrors should be able to continue to use those services.
New query engines have been developed by the RCSB, and these will be introduced during the transition year. The aim of these query engines is to provide basic and more complex query capabilities for the PDB in convenient forms. The basic level query engine is called SearchLite. This keyword-based query system is the subject of an article in this newsletter. (See "New PDB Web Tools.") Although the scope of the SearchLite query engine is to provide basic query capability, this engine nevertheless exposes the information content and accompanying services provided by the RCSB PDB. The SearchLite query engine is available from the RCSB PDB Web site, and we encourage users to try it out.
A prototype version of a query engine that supports more advanced queries has been developed, and alpha testing is beginning. This engine will be made available in two phases later this year after a thorough testing and evaluation process.
During the transition period, the PDB will be accessible from two Web sites: one reflecting the RCSB PDB and one reflecting the BNL PDB. Both sites will maintain the current version of the PDB FTP archive. The FTP archive will remain in its current form.
The RCSB PDB Web site provides the PDB FTP archive, up-to-date transition information, and access to new features of the RCSB PDB system as they become available. These new features, described below, will include more complex query searching, a new data deposition tool, and a structure validation server.
The BNL PDB Web site will provide the PDB FTP archive, AutoDep, PDB Lite, and 3DB Browser and its related resources.
Structures will be released weekly by the RCSB to all PDB Web sites.
In the future, additional RCSB mirrors will be made available.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
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