Documentation

• PDB File Format - Contents Guide Version 3.20 (Sept 15, 2008)
  
  • PDF - US Letter | PDF - A4 | HTML
  • Version 3.20 Changes from 3.1 Guide (Sept 15, 2008) PDF
  
  
• Version 3.15 Changes from 3.20 Guide (Nov 18, 2008) PDF
  
  
• PDB File Format - Contents Guide Version 3.1 (Feb 2008 for data released after Aug 1, 2007)
  This document lists changes from version 2.3 PDF
  
  
• PDB File Format - Contents Guide Version 3.0 (Mar 2007 for 2007 remediation)
  
  • PDF | HTML
  
  
• PDB File Format - Contents Guide Version 2.3 (Jul 09, 1998 for data released 1998 - Jul 2007)
  
  • PDF - US Letter | PDF - A4 | HTML
  
  
• PDB Exchange Dictionary/PDBx - version 1.0670 as of Mar 2009
  
  
• PDBML/XML - version 1.0670 as of Mar 2009
  
  
• The original Protein Data Bank Contents Guide was authored by J. Callaway, M. Cummings, B. Deroski, P. Esposito, A. Forman, P. Langdon, M. Libeson, J. McCarthy, J. Sikora, D. Xue, E. Abola, F. Bernstein, N. Manning, R. Shea, D. Stampf, and J. Sussman (1996) Brookhaven National Laboratory. Historical copies of the PDB file format from 1992 and 1996 are available.

• Processing Procedures (PDF) version 2.3 as of Mar 2009
  
  
• Annotation Policies (PDF) version 2.3 as of Mar 2009
  
  

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).