wwPDB Remediation

A major focus of the wwPDB is maintaining consistency and accuracy across the archive. As the PDB grows, developments in structure determination methods and technologies can challenge how all structures are represented. The wwPDB addresses these challenges with regular reviews of data processing procedures and coordinates remediation efforts to improve data representation.

The July 2011 release of Version 4.0 of the PDB archive involved remediating complex problems, including the representation of biological assemblies, residual B factors, peptide inhibitors and antibiotics, and entries in nonstandard crystal frames. A description of the review and resulting changes and corrections is available in a PDF document. Any changes made to the data are recorded in the PDBX_VERSION data category and in a revision log created for this release (XLS and CSV).

The March 2009 release of Version 3.2 of the PDB archive includes improvements and enhancements to the data, including details about the chemistry of the polymer and the ligands bound to it, biological assemblies, and binding sites of ligands and metal ions. An overview (PDF) is provided.

In August 2007, the wwPDB released remediated files for all PDB entries to ensure the uniformity of the data across the archive. As a part of this project, many entries in the archive were updated and made consistent, with a focus on sequences (references to databases and taxonomies, plus differences between chemical and macromolecular sequences); primary citations; and assembly and virus information. In the Chemical Component Dictionary, the chemistry and nomenclature in monomers and ligands was standardized. This release of remediated data greatly improved searching and reporting capabilities across the PDB archive.

The details of this project have been described in

K. Henrick, Z. Feng, W. Bluhm, D. Dimitropoulos, J.F. Doreleijers, S. Dutta, J.L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C.L. Lawson, J.L. Markley, H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E.L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin, and H. Berman (2008) Remediation of the Protein Data Bank Archive. Nucleic Acids Res. 36(Database issue): D426-D433.

C.L. Lawson, S. Dutta, J.D. Westbrook, K. Henrick, and H.M. Berman (2008) Representation of viruses in the remediated PDB archive. Acta Cryst. D64: 874-882.

The full scope of the remediation project is also available an Overview Document (PDF).