wwPDB News

08-May-2008

Workshop on Next Generation Validation Tools for the wwPDB

A meeting of the wwPDB X-ray Validation Task Force was held to collect recommendations and develop consensus on additional validation that should be performed on PDB entries, and to identify software applications to perform validation tasks.

The workshop was organized by Randy Read (Cambridge University), and sponsored by the RCSB PDB & PDBe. Detailed information about the workshop is available at http://www.wwpdb.org/workshop/2008/index.html.

21-April-2008

Recent wwPDB Papers

Data deposition and annotation at the Worldwide Protein Data Bank. Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, Helen M. Berman (2008) in Methods in Molecular Biology, vol. 426: Structural Proteomics: High-Throughput Methods (Bostjan Kobe, Mitchell Guss, Thomas Huber, eds.), pp. 81-101.

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. John L. Markley, Eldon L. Ulrich, Helen M. Berman, Kim Henrick, Haruki Nakamura, and Hideo Akutsu (2008) J Biomol NMR 40(3): 153-155

PDB Archives More Than 50,000 Structures

With this week's update, the PDB archive reached a significant milestone in its 37-year history. The 50,000th molecule structure was released into the archive, joining other structures vital to pharmacology, bioinformatics, and education.

The worldwide Protein Data Bank (wwPDB) has seen the archive double in size since 2004. The PDB was founded in 1971 with seven structures at Brookhaven National Laboratory. Today, the wwPDB receives approximately 25 new experimentally-determined structures from scientists each day for inclusion in the archive. More than 5 million files are downloaded from the PDB archive every month. Users include structural biologists, computational biologists, biochemists, and molecular biologists in academia, government, and industry as well as educators and students.

It is estimated that the size of the PDB archive will triple to 150,000 structures by the year 2014.

The 50,000th structure was released a week after another milestone event--the publication of the 100th edition of the Molecule of the Month.

Proteins, one of the main building blocks for living organisms, come in a variety of shapes, with the form of a protein corresponding to its function. The structures housed in the PDB demonstrate great diversity in size, complexity, and function, including:

• Insulin, the protein deficient in diabetic patients
• p53 tumor suppressor, a protein often implicated in cancer
• Anthrax toxin, the disease-causing protein made by anthrax
• Amyloid peptide, a protein implicated in Alzheimer's disease
• Influenza proteins, structures which may help scientists design medicines to combat the flu
• Prion proteins, misshapen proteins that are the cause of many diseases, including mad cow disease

Time-stamped Copies of PDB Archive Available via FTP

A time-stamped snapshot of the PDB archive (ftp://ftp.wwpdb.org) as of January 7, 2008 has been added to ftp://snapshots.rcsb.org/.

Snapshots of the PDB have been archived annually since 2004. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

The script at ftp://snapshots.rcsb.org/rsyncSnapshots.sh may be used to make a local copy of a snapshot or sections of the snapshot.

The directory 20080107 includes the 48,161 experimentally-determined coordinate files that were current as of January 7, 2008. Coordinate data are available in PDB, mmCIF, and XML formats. The date and time stamp of each file indicates the last time the file was modified.

Announcement: Data Processing Versioning Procedures

Data in the PDB archive currently follow either PDB File Format Version 3.0 or 3.1. This is indicated in REMARK 4 of the file.

Version 3.0 is the format used for files released as a result of the Remediation Project.

Since August 1, 2007, all files processed and released into the archive follow Version 3.1. When modifications are made to files released prior to that date, they are then re-released in Version 3.1.

Version 3.1 differs in descriptions of the biological unit (REMARK 300/350), geometry (REMARK 500), atom/residues modeled as zero occupancy (REMARK 475/480), non-polymer residues with missing atoms (REMARK 610), and metal coordination (REMARK 620). Documentation describing the differences between these versions is available at http://www.wwpdb.org/docs.html.

Beginning March 4, 2008, it will be indicated in the REVDAT record with the name "VERSN" when a Version 3.0 file is re-released as Version 3.1.

For example, if the journal record is updated in an entry that still follows Version 3.0, the REVDAT would appear as:

REVDAT 1 04-MAR-08 1ABC 1 JRNL VERSN
REVDAT 1 13-FEB-07 1ABC 0

There is no change to how depositors submit their files. Any required changes in nomenclature can be made automatically by the wwPDB during the annotation process.

Documentation about file formats and the Remediation Project is available at www.wwpdb.org.

wwPDB Paper Published

"Remediation of the protein data bank" archive describes the scope and methods of the wwPDB's Remedation Project

K. Henrick; Z. Feng; W. F. 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; H. M. Berman Nucleic Acids Research 2008 36(Database issue):D426-D433; doi:10.1093/nar/gkm937

Announcement: Experimental Data Will Be Required for
Depositions Starting February 1, 2008

Effective February 1, 2008, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) will a mandatory requirement for PDB deposition.

These data must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/msd), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu).

Data can be released as soon as they have been processed and approved. There is a one-year limit on the length of time a structure and its experimental data can be put on hold, including structures that are on hold until the associated paper is published (HPUB).

This policy was developed as a result of comments and recommendations from the PDB user community, including the Commission on Biological Macromolecules of the International Union of Crystallography and the NMR Task Force, and has been endorsed by the wwPDB Advisory Committee.

Questions relating to depositions should be sent to info@wwpdb.org.

Advisory Committee Meeting

The world wide Protein Data Bank Advisory Committee (wwPDBAC) met in Princeton, NJ on September 7, 2007. The presentations by wwPDB members and the report from the wwPDBAC are available. After this meeting, a "Funding Forum" took place. At this forum, the wwPDB AC sought advice on funding options for the continued operation of the wwPDB organization from the representatives present from the agencies that fund the individual groups. A report from that meeting is also available.

wwPDB Paper Published

Realism about PDB Nature Biotechnology 25, 845 - 846 (2007)

Remediated PDB Archive Released

The PDB archive has been remediated by the wwPDB. It is available at ftp://ftp.wwpdb.org.

All data in the PDB archive reflects the new features incorporated as part of this wwPDB project, including standardized IUPAC nomenclature for chemical components. Users may have to download new software to view the files with the new nomenclature (e.g., RasMol, Chimera). Please see http://remediation.wwpdb.org/software.html for details.

A snapshot of the unremediated PDB archive (as of July 31, 2007) will be available at ftp.rcsb.org.

Many thanks to the PDB community for all of the feedback on this project.

Remediated PDB Archive To Be Released on August 1, 2007

The PDB archive has been remediated and will be available starting August 1, 2007 from ftp://ftp.wwpdb.org.

All data in the PDB archive will reflect the new features incorporated as part of this wwPDB project, including standardized IUPAC nomenclature for chemical components.

Users may have to download new software to view the files with the new nomenclature (e.g., RasMol, Chimera). Please see http://remediation.wwpdb.org/software.html for details.

A snapshot of the unremediated PDB archive (as of July 31, 2007) will be available at ftp://ftp.rcsb.org.

An FAQ about this project and transition is available at http://www.wwpdb.org/docs.html. Questions may also be sent to info@wwpdb.org.

Announcement: Data Processing Procedures

Starting August 1, 2007, files processed and released into the archive by the wwPDB sites will reflect the new features incorporated as part of the remediation project. These files will follow the PDB Exchange Dictionary (PDBx) v1.045 and the Protein Data Bank Contents Guide Version 3.1.

There is no change to how depositors submit their files. Any required changes in nomenclature can be made automatically by the wwPDB during the annotation process.

24-Apr-2007

Announcement: Release of Remediated PDB Data

The wwPDB (www.wwpdb.org) has collaborated on a project to remediate the PDB archive and create a new set of corrected files.

The entire archive has 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 and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards.

A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http://www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with the current production site at ftp://ftp.rcsb.org. Both sites share the same directory structure. Starting May 1, the remediated data will be served using gzip compression.

Your input is very important to us. PDB users are encouraged to test the remediated data files between April and July 2007. The details of the final transition will be announced on this website.

Detailed information about this project can be found at http://remediation.wwpdb.org.

Comments about the files should be sent to info@wwpdb.org. Major announcements will be made at the wwPDB website (http://www.wwpdb.org) as well as on the individual member websites.

The directory 20070102 includes the 40,933 experimentally-determined coordinate files that were current (i.e., not obsolete) as of January 2, 2007. Coordinate data are available in PDB, mmCIF, and XML formats. The date and time stamp of each file indicates the last time the file was modified.

Scripts are available to automatically download data:

• ftp://snapshots.rcsb.org/rsyncSnapshots.sh
  Makes a local copy of an annual snapshot or sections of the snapshot. Downloading the entire archive can be lengthy (18+ hours), but the time required to download data in a single format should be much less. Depending upon network speed, our tests show that all of the coordinate files in PDB format from a snapshot can be downloaded in about 2 1/2 hours.
  
  
• ftp://ftp.rcsb.org/pub/pdb/software/rsyncPDB.sh
  Copies the current contents of the entire archive.
  
  
• ftp://ftp.rcsb.org/pub/pdb/software/getPdbStructures.pl
  Copies portions of the current archive.
  
  
• ftp://ftp.rcsb.org/pub/pdb/software/getPdbUpdate.pl
  Copies the data from the weekly updates.

Entries in the PDB archive have been processed by the three members of the wwPDB (RCSB PDB, PDBe, and PDBj).

wwPDB members work to annotate all data deposited to the PDB archive. Information about data file formats, annotation procedures, and remediation efforts are described below.

• File Format Guides
  
  Documentation for the different file formats for PDB data is available at http://www.wwpdb.org/docs.html
  
  Entries in PDB format comply with the PDB Contents Guide v2.3 (July 1998).
  Entries in mmCIF format comply with the PDB Exchange Dictionary v1.037 (January 2007).
  Entries in XML format comply with the PDBML Schema v1.037 (January 2007).
  
  
• Annotation Procedures
  
  Annotation procedures and policies are described at http://www.wwpdb.org/docs.html
  
  There are some data items for which the processing procedures are ambiguous. Over the course of the last 12 months, the annotation teams have worked to formalize many aspects of PDB annotation policies and procedures. As a result, a consistent set of annotation procedures are being defined.
  
  
• Remediation
  
  Remediation project information is available at http://remediation.wwpdb.org/.
  
  All existing entries have been reviewed and errors have been corrected where possible. One major change is that the atomic names will conform to IUPAC standards. In addition, the chemical component dictionary has been updated and extended to include more information about the chemical structures of each component. The wwPDB Advisory Committee has reviewed and approved this effort.
  
  Please consult this site to review test data files and the new dictionary. The full new data set in PDB, mmCIF and XML formats will become available for review in April 2007.

Questions about these projects should be sent to info@wwpdb.org.

The third meeting of the world wide Protein Data Bank Advisory Committee (wwPDBAC) was held in Tokyo, Japan on October 27, 2006. The report of the meeting is available in PDF format.

A paper describing the wwPDB – data deposition and access information, data uniformity efforts, and more – has been published:

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Helen Berman; Kim Henrick; Haruki Nakamura; John L. Markley
Nucleic Acids Research 2006; doi: 10.1093/nar/gkl971

Effective October 15, 2006, PDB depositions will be restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules. This policy was recommended and endorsed by a working group comprised of structural and computational biologists and endorsed by the wwPDB advisory committee. Thus, theoretical model depositions (such as models determined purely in silico using, for example, homology or ab initio methods) will no longer be accepted.

Theoretical models that have been previously released or that will be released from now until October 15, 2006 will continue to be publicly available via the existing models archive at ftp://ftp.rcsb.org/pub/pdb/data/structures/models/current/.

A summary of the implementation plan for the phasing out of theoretical models is available in HTML and PDF formats. A paper describing the outcome of the Workshop on Archiving Structural Models of Biological Macromolecules will be available in the August 16 issue of Structure¹.

Questions about this transition should be sent to info@wwpdb.org.

^1.H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, J. Roland L. Dunbrack, K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, and J.D. Westbrook (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 14: 1211-1217.

Data from X-ray crystallographic, NMR, and cryo-electron microscopic experiments are deposited to the PDB archive by scientists from all over the world.

PDB data are processed by an international effort involving members of the wwPDB – the RCSB PDB, the Macromolecular Structure Database (MSD) at the EMBL's European Bioinformatics Institute, and Protein Data Bank Japan (PDBj). wwPDB annotators work with these data to make sure they are represented in the PDB archive in the best way possible. They run a series of checks, make corrections, and correspond with the depositors in an effort to make the data public as quickly and accurately as possible.

Statistics about the number of structures deposited, processed, and released by the wwPDB are available at http://www.wwpdb.org/stats.html.

The second meeting of the world wide Protein Data Bank Advisory Committee (wwPDBAC) was held in Florence, Italy on August 30, 2005. The report of the meeting is available in PDF format.

Starting with January 2005, time-stamped yearly snapshots of the PDB Archive will be available from ftp://snapshots.rcsb.org/. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

Currently, the directory 20050106 is available. This directory contains the exact and complete contents of the FTP archive as it appeared on January 6, 2005. This includes the 29040 experimentally-determined coordinate files that were current (i.e., not obsolete) in PDB and mmCIF formats. Data in XML (PDBML) format are not included in this first snapshot, but will be made available on DVD in the near future. Subsequent snapshots on this FTP server will include data in PDB, mmCIF, and PDBML formats.

The snapshot follows the historical directory structure -- coordinate files are contained in subdirectories named after the two middle characters of the PDB ID, for example, 100d is found in the directory '00'.

The date and time stamp of each file indicates the last time the file was modified. Entries in the PDB archive have been processed by the three members of the wwPDB (RCSB, PDBe, and PDBj).

The first meeting of the world wide Protein Data Bank Advisory Committee (wwPDBAC) was held in Washington, D.C. on November 21, 2004. The report of the meeting is available in PDF format.

Today the Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database at the EMBL's European Bioinformatics Institute (PDBe), and Protein Data Bank Japan (PDBj) announced a collaboration to form the Worldwide Protein Data Bank (wwPDB; http://www.wwpdb.org/). The announcement is published in the December issue of Nature Structural Biology [H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980].

The collaboration reflects the growing international and interdisciplinary nature of scientific research, and formalizes the global character of the PDB, which has been used as an international resource for the collection and sharing of three-dimensional information on proteins and other large molecules since its inception 32 years ago. The formation of the wwPDB will be transparent to users and will ensure the overall quality and consistency of data directly available through the PDB.

"By providing a formal mechanism for standardizing the presentation of PDB data, software developers and users of the data will be assured of consistent data. At the same time, it is hoped that this wwPDB will allow for individual creativity in how the data are presented and made available to the community," said Helen Berman, director of the RCSB PDB and Board of Governors Professor of Chemistry at Rutgers, The State University of New Jersey.

Kim Henrick, head of the PDBe said, "The PDB is a canonical research resource that transcends both scientific and political boundaries. The wwPDB agreement among the three equal partners elevates the responsibility for the deposition and accessibility of the data to a global level. The EBI has been a longtime deposition site and advisor to the PDB and the evolution of that role is a welcome development."

Head of the PDBj group at the Institute for Protein Research in Osaka University, Haruki Nakamura said, "The PDBj has become the representative for the PDB throughout Asia and Oceania. With the recent explosion of interest in structural biology and bioinformatics research in the region, which would not be possible without the PDB, it is a natural step for us to formalize our involvement through the wwPDB."

The PDB is the single archive of biological macromolecular structure data, which is made freely and publicly available to researchers, educators, and students. Worldwide, the PDB receives over 60 million hits per year. As of October 28, 2003, it contained 22,984 structures, a number that has been growing exponentially.

According to a 10-year agreement signed by the 3 founding members of the wwPDB, the sites will share responsibilities in data deposition, data processing, and distribution. An international advisory board will be formed to support the collaboration.