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wwPDB 2012 News

Contents

21-December-2012 Announcement: Remediation of Structure Factor Data and Release Plan
18-December-2012 Announcement: EMDB header format update
11-December-2012 New Reference Dictionary for Biologically Interesting Molecules Released
3-December-2012 Announcement: Experimental Data Release Policy Clarification
17-October-2012 Announcement: New Reference Dictionary for Biologically Interesting Molecules to be Released on FTP December 2012
17-October-2012 Nobel Prize Awarded for studies of G-protein-coupled receptors
10-September-2012 Future Funding of the BioMagResBank: White Paper and Community Discussions
29-August-2012 PDB Validation Reports Part of JBC Manuscript Submission
29-August-2012 Special Symposium on PDB: Basis for Life Science and Drug Development
29-August-2012 Science as an open enterprise
16-March-2012 wwPDB Milestones: 80,000 Entries Released, PDB40 Meeting Report Published
6-March-2012 EM Data Bank joins the PDB archive
8-February-2012 A vision for validation of 3DEM maps and map-derived models
10-January-2012 Time-stamped Copies of the PDB Archive

Previous announcements are available for 2011 and for 2003-2010.



21-December-2012

Announcement: Remediation of Structure Factor Data and Release Plan

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.

Starting January 16, 2013, the wwPDB will begin to release these modified structure factors in weekly batches of 1000. These files will be available from ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/structure_factors/.

Questions should be sent to info@wwpdb.org.

18-December-2012

Announcement: EMDB header format update

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.

We are announcing this planned change in advance so that developers can make any necessary modifications to software/services that make use of EMDB header files. Please contact us at help@emdatabank.org with any questions or concerns.

The candidate schema is available for download here: ftp://ftp.ebi.ac.uk/pub/databases/emdb/doc/XML-schemas/Header-schema/candidate/emdb.xsd. A complete list of changes can be found at the beginning of the schema file.

Example header files using the new format can be found here: ftp://ftp.ebi.ac.uk/pub/databases/emdb/examples1.9.0.

v. 1.9.0 EMDB xml schema highlights:

  • Two new descriptors 'method' and 'specimen state' allow a map to be separately defined by both its specimen state and reconstruction methodology. These replace 'aggregation state' descriptor of v.1.8 and earlier schema versions, which mixed this information and did not permit, e.g., tomography on 2D crystals or subtomogram averaging on helical samples.
  • The methodology descriptor now explicitly includes tomography and subtomogram averaging as enumeration values.
  • Obsolete/supersede entry information is now provided.

11-December-2012

New Reference Dictionary for Biologically Interesting Molecules Released

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.

This Biologically Interesting molecule Reference Dictionary (BIRD) contains chemical descriptions, sequence and linkage information, and functional and classification information as taken from the core structures and from external resources. PDB entries containing these molecules have been annotated using this dictionary, and will contain a corresponding BIRD ID code only in the PDBx-formatted file.

BIRD is available on the wwPDB FTP server adjacent to the Chemical Component Dictionary at ftp://ftp.wwpdb.org/pub/pdb/data/bird/prd/.

The use of BIRD will greatly improve the consistency of peptide-like antibiotic and inhibitor molecules in the PDB.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.

3-December-2012

Announcement: Experimental Data Release Policy Clarification

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

Questions should be sent to info@wwpdb.org.

17-October-2012

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

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.

This Biologically Interesting molecule Reference Dictionary (BIRD) contains chemical descriptions, sequence and linkage information, and functional and classification information as taken from the core structures and from external resources. PDB entries containing these molecules will be annotated using this dictionary, and will contain a corresponding BIRD ID code only in the PDBx-formatted file.

BIRD will be available on the wwPDB FTP server adjacent to the Chemical Component Dictionary.

The use of BIRD will greatly improve the consistency of peptide-like antibiotic and inhibitor molecules in the PDB.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.

17-October-2012

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

image of PDB ID 3SN6

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.

Learn more about this award and related structures at PDBe, PDBj, and the RCSB PDB.


10-September-2012

Future Funding of the BioMagResBank: White Paper and Community Discussions

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:

Editorial: The BMRB matters (2012) NSMB 19: 853 doi:10.1038/nsmb.2387

Community Comments: In support of the BMRB (2012) NSMB 19: 854 - 860 doi:10.1038/nsmb.2371

From the BMRB: White Paper on Future Funding (doc)

This issue has also been discussed elsewhere (Nature, The Scientist, Corante)

The BMRB, housed at the University of Wisconsin - Madison, collects, annotates, archives, and disseminates the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites.

Current funding from the National Library of Medicine is set to expire in 2014. It appears critical that a funding plan be developed within the coming year.

29-August-2012

PDB Validation Reports Part of JBC Manuscript Submission

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

Validation reports are also required by International Union of Crystallography (IUCr) journals as part of their submission process.

wwPDB members currently 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 for easy sharing and review.

The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures and the wwPDB Common Deposition & Annotation Tool.

More information about JBC's requirement can be found at ASBMB Today. Example reports are available from the wwPDB.

29-August-2012

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

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.

Presentations will include:

wwPDB and its Impacts on Science and Society, Haruki Nakamura, Osaka University

Impact of the Protein Data Bank on Drug Discovery, Stephen Kevin Burley, University of California at San Diego

Molecular Nanomachines in Living Organisms-Exquisite Structural Design far beyond State-of-the-Art Nanotechnology, Keiichi Namba, Osaka University

A meeting flyer is available (Japanese | English). Please contact the wwPDB for more information.

The symposium is organized by the wwPDB Foundation, and is sponsored by the National Bioscience Database Center-Japan Science and Technology Agency; Institute for Protein Research, Osaka University; Graduate School of Frontier Biosciences, Osaka University; The Biophysical Society of Japan; Protein Science Society of Japan; and the Osaka Pharmaceutical Manufacturers Association.

29-August-2012

Science as an open enterprise

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.

The full report, entitled Science as an open enterprise, is online.

16-March-2012

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

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.

In 2011, 8865 entries were deposited and annotated, while 8107 were released.

wwPDB deposition and download statistics are updated regularly.

Meeting Report
A review of the PDB40 meeting has been published:

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley Structure (2012) 20: 391 - 396

Selected presentations and related details from the meeting are also available from http://www.wwpdb.org/PDB40.html.

6-March-2012

EM Data Bank joins the PDB archive

pdb-emdb image

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.

The merger makes 3DEM results available in a single archive, including over 1300 electron microscopy derived maps from EMDB and 400 coordinates for EM map-derived models in PDB. It is also an essential step in the wwPDB's development of a Common Deposition & Annotation Tool that will cover all experimental methods, including hybrid methods.

With the addition of EMDB data, the physical size of the complete wwPDB archive jumps to roughly 180 GB (from its previous 130 GB). Sites that mirror the full wwPDB archive will need to increase storage capacity accordingly.

Summary information regarding the merger and detailed specifications for data access are posted at wwpdb.org/em/.

8-February-2012

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

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).

The inaugural meeting of the EM VTF, organized by EMDataBank, Unified Data Resource for 3DEM, was held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. An international group of 3DEM experts explored how to assess maps, models, and other data that are deposited into the EM Data Bank (EMDB) and Protein Data Bank (PDB) public data archives. The 2-day workshop was co-chaired by Richard Henderson (MRC, Cambridge) and Andrej Sali (UCSF).

For deposited maps, the EM VTF recognized a critical need to develop standards for assessing map resolution and accuracy, and recommended reporting of map resolution in accordance with visible features, deposition of annotations specific to each map type, and validation of map symmetry.

For deposited map-derived models, EM VTF recommendations include establishment of criteria for assessing models both with and without regard to the fit to the map, creation of community-wide benchmarks for modelling methods, sequence annotation of all map components, and capability to archive coarse-grained representations of models.

Additional recommendations include establishing deposition guidelines for publication of 3DEM structures in journals, and expanding the role of EMDataBank to work together with the 3DEM community to provide unified access to 3DEM structures and to facilitate development of validation and data standards.

This initial report by the EM VTF follows closely on the heels of recommendations by the wwPDB X-ray VTF published last year (Structure, 2011 19: 1395-1412). Additional task forces have been convened for NMR and small angle scattering methods.

The efforts of all of the report authors are greatly appreciated: Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson.

EMDataBank, Unified Data Resource for 3DEM (http://www.emdatabank.org), was established in 2007 and is a joint effort of the Protein Data Bank in Europe (PDBe) at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) at Rutgers, and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine, and is funded by the National Institutes of Health. EMDataBank serves the 3DEM and wider scientific communities with its 3DEM-specific portal for deposition and access to EM-derived structures and links to software, validation standards and conventions. The new report will serve as EMDataBank's roadmap for development of validation standards for data in 3DEM public data archivs in collaboration with the 3DEM community.

10-January-2012

Time-stamped Copies of the PDB Archive

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.

The directory 20120102 includes the 78,237 experimentally-determined coordinate files and related experimental data that were available at that time. 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.

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


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