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The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), PDBe (Europe) and PDBj (Japan)1. The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.

This site provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.

Please note: ftp://ftp.rcsb.org is no longer updated. Please access the PDB archive using one of the FTP sites listed in the left menu.

25-September-2009
wwPDB FTP Advisory Notice

This advisory notice describes four changes to the content of the wwPDB FTP site. The changes described here will become effective on Nov 24, 2009.

  1. The script for mirroring the FTP site using the RSYNC program has been updated. The new script has been modified to prompt the user to choose one of three rsync servers (RCSB PDB, PDBe, PDBj). The rsync script has the following URLs:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/software/rsyncPDB.sh
    PDBe: ftp://ftp.ebi.ac.uk/pub/databas es/rcsb/pdb-remediated/software/rsyncPDB.sh
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/software/rsyncPDB.sh

  2. The top-level README file has been updated to point to an expanded set of download instructions hosted on the wwPDB website. The URL for the download instructions is:

    wwPDB website: http://www.wwpdb.org/downloads.html

    The URLs for the updated README file are located at:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/README
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/README
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/README

  3. The directories containing newsletters have been updated. Newsletters can be found in the following URLs:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/doc/newsletters/
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/doc/newsletters/
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/doc/newsletters/

  4. Sequence cluster data that is used only by the RCSB PDB website has been relocated to an RCSB PDB resource site. This data was formerly located at the following URLS:

    RCSB PDB: ftp://ftp.wwpdb.org/pub/pdb/derived_data/NR/
    PDBe: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/derived_data/NR/
    PDBj: ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/derived_data/NR/

The new URL for this data is:

RCSB PDB: ftp://resources.rcsb.org/sequence/clusters/


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Questions? info@wwpdb.org

1. H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980


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