MESSAGE FROM THE RCSB PDB

The wwPDB is pleased to announce that the PDB archive (ftp://ftp.wwpdb.org) is now comprised of remediated data.

In the past, query across the complete PDB archive has been limited by missing, erroneous and inconsistently reported data, nomenclature, and other annotations. The evolution of experimental methods and the techniques used to process these data has introduced various inconsistencies into the PDB archive.

Over the years, wwPDB members – the RCSB PDB, MSD-EBI, PDBj, and BMRB – have worked together to ensure the uniformity of entries archived in the PDB. The entire archive has now been reviewed and remediated with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical the macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments.

As these corrections were being incorporated, the wwPDB worked with software developers and database maintainers to ensure a smooth transition. This year, the remediated archive was made public for testing, and the resulting feedback was incorporated into the archive. The wwPDB greatly appreciates the efforts of the many people who have taken the time to review and work with these data files, and the advice and discussions with our advisory committees.

Descriptions of this remediation process are available in this newsletter and at the wwPDB site at www.wwpdb.org.