wwPDB News

10,000 NMR Structure Milestone Reached

Tuesday, 19 June 2013 09:00:00 PST

The wwPDB is excited to announce that the number of structures available in the PDB archive determined using NMR spectroscopy has passed the 10,000 mark.

Small Angle Scattering Task Force

Wednesday, 12 June 2013 16:00:01 GMT

We are pleased to announce that the Report of the wwPDB Small-Angle Scattering Task Force, "Data Requirements for Biomolecular Modeling and the PDB Structure", has been published in the journal Structure (doi:10.1016/j.str.2013.04.020).

Landmark HIV Capsid Structures Released in PDB

Thursday, 30 May 2013 16:00:01 GMT

Two complete HIV-capsid structures, both of unprecedented size, are described in this week's issue of Nature and released in the Protein Data Bank (PDB; wwpdb.org). This represents a significant advance in the field of structural biology and a milestone for the PDB.

Deposition and Release of PDB Entries Containing Large Structures

Wednesday, 22 May 2013 16:00:01 GMT

In order to meet the challenges of ever greater numbers of PDB depositions, involving ever larger and more complex structures, often determined using multiple methods, the Worldwide Protein Data Bank partners (wwPDB; http://wwpdb.org/) are developing a completely new system for deposition and annotation of PDB entries. This new system will go into full production at all the wwPDB deposition sites early in 2014 and will then be able to handle depositions of structures of any size, determined using diffraction, NMR and/or EM methods. Large structures will also be processed and released intact so that "split entries" become a thing of the past.

The Biologically Interesting Molecule Reference Dictionary (BIRD) for Peptide-like Antibiotic and Inhibitor Molecules

Wednesday, 3 April 2013 00:00:01 GMT

The wwPDB's Biologically Interesting molecule Reference Dictionary (BIRD) describes antibiotics, peptide inhibitors, and other complex biological ligands. To help define and represent these biologically interesting molecules, BIRD contains chemical descriptions, sequence and linkage information, and functional and classification information as taken from the core structures and from external resources.

Special issue of Biopolymers Continues PDB40 Celebration

Thursday, 7 March 2013 00:00:01 GMT

The March 2013 issue of Biopolymers contains six invited contributions based on presentations made at the October 2011 symposium held at Cold Spring Harbor Laboratory that commemorated 40 years of the Protein Data Bank archive.

Time-stamped Copies of the PDB Archive

Thursday, 7 March 2013 00:00:01 GMT

A snapshot of the PDB archive (ftp.wwpdb.org) as of January 1, 2013 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.

Announcement: Remediation of Structure Factor Data and Release Plan

Saturday, 22 December 2012 00:00:01 GMT

The wwPDB has reviewed structure factor files in the archive for format consistency and correspondence with coordinate data. As a result, around 43,800 structure factor files have been updated to standardize the format and to incorporate data corrections. Changes made are described in the audit.details record of the structure factor file.

Announcement: EMDB header format update

Wednesday, 19 December 2012 00:00:01 GMT

On 16 January 2013, the EMDB archive plans to adopt an updated format, v.1.9.0, for the entry header file (XML file associated with each map). This means that EMDB header files distributed from wwPDB partner sites will conform to the 1.9.0 format, and EMDataBank deposition/annotation/search services will start using this format.

New Reference Dictionary for Biologically Interesting Molecules Released

Wednesday, 12 December 2012 00:00:01 GMT

The wwPDB has reviewed the representation of peptide-like antibiotic and inhibitor molecules in the PDB archive. As a result, a new reference dictionary has been created to help define and represent these biologically interesting molecules.

Announcement: Experimental Data Release Policy Clarification

Monday, 3 December 2012 00:00:01 GMT

Effective February 6, 2013, coordinates and experimental data deposited in the PDB will follow the same release status.

Announcement: New Reference Dictionary for Biologically Interesting Molecules to be Released on FTP December 2012

Wednesday, 17 October 2012 00:00:01 GMT

Nobel Prize Awarded for studies of G-protein-coupled receptors

Wednesday, 17 October 2012 00:00:01 GMT

The 2012 Nobel Prize in Chemistry was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka for studies of G-protein-coupled receptors. The PDB holds many GPCRs, such as Kobilka's groundbreaking structure of the beta2 adrenergic receptor-Gs protein complex shown here.

Future Funding of the BioMagResBank: White Paper and Community Discussions

Monday, 10 September 2012 00:00:01 GMT

A white paper on the future funding of the BMRB and related articles have been published in the latest issue of Nature Structural & Molecular Biology.

PDB Validation Reports Part of JBC Manuscript Submission

Thursday, 30 August 2012 00:00:01 GMT

The Journal of Biological Chemistry (JBC) now requires authors to submit a validation summary report along with manuscripts describing X-ray crystallographic structure studies.

Special Symposium on PDB: Basis for Life Science and Drug Development

Thursday, 30 August 2012 00:00:01 GMT

A special PDB symposium will be held on Saturday, October 13, 2012 at Hearton Hall in Osaka, Japan. The meeting is free and open to the public.

Science as an open enterprise

Thursday, 30 August 2012 00:00:01 GMT

The wwPDB's management of the PDB archive was highlighted as a major international data initiative with well defined protocols for the selection and incorporation of new data and access to them in a report from The Royal Society on openness in scientific data.

wwPDB Milestones: 80,000 Entries Released, PDB40 Meeting Report Published

Saturday, 17 March 2012 00:00:01 GMT

The Archive Grows With the March 13, 2012 update, 80,041 PDB entries became available in the archive. The PDB hit the 70,000 mark in December 2010.

EM Data Bank joins the PDB archive

Wednesday, 7 March 2012 00:00:01 GMT

The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, has joined the PDB archive (ftp://ftp.wwpdb.org), as announced previously.

A vision for validation of 3DEM maps and map-derived models

Thursday, 9 February 2012 00:00:01 GMT

We are pleased to announce the publication of the outcome of the first Electron Microscopy Validation Task Force (EM VTF) meeting in the journal Structure: Henderson et al., Structure (2012).

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