wwPDB News

Time-stamped Copies of the PDB Archive

Wednesday, 11 January 2012 00:00:01 GMT

A snapshot of the PDB archive (ftp.wwpdb.org) as of January 2, 2012 has been added to ftp://snapshots.wwpdb.org/. Snapshots have been archived annually since January 2005 to provide readily identifiable data sets for research on the PDB archive.

EM Data Bank to join the PDB archive

Wed, 21 December 2011 00:00:01 GMT

The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, will join the PDB archive on 7 March 2012.

PDB40 Symposium Update

Wed, 26 October 2011 00:00:01 GMT

Celebrate four decades of innovation in structural biology with the wwPDB October 28-30, 2011 at CSHL. View the updated program (PDF from 10/24) and poster abstracts (PDF). Limited space is available--register today!

First contours of a vision for the future of validation at the PDB

Sat, 15 October 2011 00:00:01 GMT

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is pleased to direct PDB depositors and users to the recommendations of the wwPDB X-ray Validation Task Force (VTF) that were published in the journal Structure this week (2011, vol. 19: 1395-1412).

PDB Depositions Can Be Targets for CAPRI

Sat, 1 October 2011 00:00:01 GMT

Depositing a protein-protein, protein-DNA, protein-RNA or protein-peptide complex? Consider submitting your structure as a target for CAPRI after depositing your entry to the PDB.

PDB 40 News: Special Anniversary at CSHL October 28-30, 2011

Sat, 1 October 2011 00:00:01 GMT

In October 2011, the wwPDB will host a scientific symposium at Cold Spring Harbor Laboratory (CSHL) to celebrate the PDB's 40th anniversary and the many scientific contributions it archives.

IUCr XXII: wwPDB Q&A session, exhibit booth, presentations, posters and more

Thur, 11 August 2011 00:00:01 GMT

Meet wwPDB directors and staff from around the globe at the XXII General Assembly and Congress of the International Union of Crystallography (IUCr, August 22-30, 2011) in Madrid, Spain.

Due Aug 1: PDB40 Travel Award Applications for Early Career Scientists and Students

Thur, 28 July 2011 00:00:01 GMT

Celebrate four decades of innovation in structural biology this fall at a Cold Spring Harbor Laboratory symposium honoring the PDB's 40th anniversary and the many scientific contributions it archives.

PDB Archive Version 4.0 Released

Sat, 14 July 2011 00:00:01 GMT

As announced previously, the wwPDB has released PDB Archive Version 4.0. These files follow the PDB Exchange Dictionary v.4.0 and contain the results of remediating complex problems, including the representation of biological assemblies, residual B factors, peptide inhibitors and antibiotics, and entries in nonstandard crystal frames.

PDB 40 News: Special Anniversary at CSHL October 28-30, 2011

Sat, 2 July 2011 00:00:01 GMT

In October 2011, the wwPDB will host a scientific symposium at Cold Spring Harbor Laboratory (CSHL) to celebrate the PDB's 40th anniversary and the many scientific contributions it archives.

Announcement: PDB Archive Version 4.0 to be Released July 13, 2011

Sat, 18 June 2011 00:00:01 GMT

As announced previously, the wwPDB has performed an ambitious review of the PDB archive resulting in a new set of corrected files that follow the PDB Exchange Dictionary v.4.0. These files will be released on the July 13, 2011.

Announcement: PDB Archive Version 4.0 to be Released Summer 2011

Thur, 14 April 2011 00:00:01 GMT

The wwPDB has performed an ambitious review of the PDB archive and has created a new set of corrected files that will be released in Summer 2011. Version 4.0 PDB entries will follow the PDB Exchange Dictionary v.4.0.

Special Symposium Celebrating the 40th Anniversary of the PDB

Tue, 15 February 2011 00:00:01 GMT

In October 2011, the Worldwide Protein Data Bank (wwPDB) will host a scientific symposium celebrating the 40th anniversary of the inception of the PDB, and the many scientific contributions it archives.

Time-stamped Copies of PDB Archive Available via FTP

Sat, 15 January 2011 00:00:01 GMT

A snapshot of the PDB archive (ftp.wwpdb.org) as of January 3, 2011 has been added to ftp://snapshots.wwpdb.org/. Snapshots have been archived annually since January 2005 to provide readily identifiable data sets for research on the PDB archive.

From 7 to 70,000: The PDB Reaches a New Milestone

Thu, 22 December 2010 00:00:01 GMT

As the year 2010 draws to a close, the number of biomacromolecular structures available in the PDB archive now exceeds 70,000.

Advanced Notification

Thu, 22 December 2010 00:00:01 GMT

From January 14, 2011, the wwPDB will resume the practice of providing advance notification of PDB entries that are about to be released.

Advisory Committee Meeting

Thu, 17 December 2010 00:00:01 GMT

The Worldwide Protein Data Bank Advisory Committee (wwPDBAC) met in Piscataway, NJ on October 1, 2010. The presentations by wwPDB members and the report from the wwPDBAC have been posted online.

Announcement: Chemical Shift Data Required for NMR Depositions Starting December 6, 2010

Wed, 6 October 2010 00:00:01 GMT

Effective December 6, 2010, deposition of chemical shift data will be mandatory when submitting NMR entries to the PDB.

Upcoming Meeting: PDB Symposium at ACS

Fri, 13 August 2010 00:00:01 GMT

On Sunday, August 22 at 1:30 p.m., The PDB and Chemistry symposium will be held as part of the American Chemical Society's Fall National Meeting (Boston Convention & Exhibition Center, Room 157C).

Validation Report PDFs

Sat, 07 August 2010 00:00:01 GMT

wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking as part of the structure annotation process. These documents are available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.

RSS Feed for wwPDB News

Wed, 14 July 2010 00:00:01 GMT

Subscribe to the wwPDB RSS (Really Simple Syndication) Feed to get the latest news as it is published. This feed pushes information to RSS readers so users can easily keep up to date with wwPDB announcements.

Version 2 NMR Restraint Files Available from the wwPDB FTP

Thu, 2 July 2010 00:00:01 GMT

A new set of NMR restraint data files have been added to the wwPDB FTP. These restraint files, identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current archive.

wwPDB To Provide Validation Reports as PDFs

Fri, 30 Apr 2010 00:00:01 GMT

As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010 these documents will be available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.

Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010

Fri, 30 Apr 2010 00:00:01 GMT

With the June 30, 2010 update, a new set of NMR restraint data files will be added to the wwPDB FTP archive (ftp://ftp.wwpdb.org, ftp://ftp.ebi.ac.uk, and ftp://pdb.protein.osaka-u.ac.jp). These restraint files, which will be identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current wwPDB archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.

Changes to the wwPDB Policy for Depositing Polypeptide Structures

Thu, 18 Feb 2010 00:00:01 GMT

The wwPDB now accepts polypeptide structure depositions of all gene products; all naturally-occuring, non-ribosomally synthesized peptides, such as antibiotics; and all peptidic repeat units of larger polymers, such as fibrous and amyloid polymers. In addition, non-naturally occurring synthetic peptides with at least 24 residues will be accepted for deposition.

wwPDB FTP Advisory Notice

Tue, 02 Feb 2010 00:00:01 GMT

The PDB archive can be accessed at FTP sites at the RCSB PDB, PDBe, and PDBj. The update schedules for these sites have been coordinated to be simultaneous. All updates now occur at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

Advisory Committee Meeting

Thu, 28 Jan 2010 00:00:01 GMT