During the past year, the wwPDB annotators have collaborated on a project to clarify the details and procedures related to data processing and annotation. The result is a PDB Contents Guide Version 3.2 that more fully describes the PDB file format. This document is available as a PDF and in HTML, and is accompanied by a document highlighting these clarifications.

In the coming months, all files released by the wwPDB will follow the format as described in this document. Details will be announced on this website.

2007 Remediation

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).