wwPDB 2010 News

Contents

21 December From 7 to 70,000: The PDB Reaches a New Milestone
21 December Advanced Notification
16 December Advisory Committee Meeting
05 October Announcement: Chemical Shift Data Required for NMR Depositions Starting December 6, 2010
12 August Upcoming Meeting: PDB Symposium at ACS
06 August Validation Report PDFs
13 July RSS Feed for wwPDB News
01 July Version 2 NMR Restraint Files Available from the wwPDB FTP
30 April wwPDB To Provide Validation Reports as PDFs
30 April Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010
18 February Changes to the wwPDB Policy for Depositing Polypeptide Structures
02 February wwPDB FTP Advisory Notice
28 January Advisory Committee Meeting

21 December, 2010

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

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

The PDB is the single, global archive for information about the 3D structure of biomacromolecules and their complexes, as determined by X-ray crystallography, NMR spectroscopy and cryo-electron microscopy, and includes more than a few Nobel Prize-winning structures. The number of entries available was only seven when the PDB was founded -- with great foresight -- at Brookhaven National Laboratory in 1971. A symposium to celebrate the 40th anniversary of this invaluable resource will be held at Cold Spring Harbor Laboratory in October 2011.

Since 2003, the PDB archive has been operated by the Worldwide Protein Data Bank (wwPDB) collaboration of organizations that act as deposition, data processing and distribution centers for PDB data. The wwPDB members are RCSB PDB (USA), PDBe (UK), PDBj (Japan), and the BMRB (USA). These organizations are the only sites that accept depositions of new biomacromolecular structures and associated experimental data. wwPDB partners also collaborate on issues of policy, formats, standards, curation procedures and validation, and are currently developing a complex new software system to meet the future demands of structure deposition and annotation. The work of the wwPDB organization is guided by an Advisory Board, with representatives of the various stakeholder communities.

Today, wwPDB partners receive approximately 25 new structure depositions per day. In 2010, more than 260 million data files were downloaded or viewed online at wwPDB partner sites. Users include structural biologists, computational biologists, biochemists, molecular biologists, and other scientists in academia, government and industry (including pharmaceutical, chemical, and biotechnology companies). PDB data are also used by educators and students for furthering their understanding of biology.

Other wwPDB highlights from 2010 include the provision of validation reports (as PDF files) to depositors and the mandatory deposition of chemical shift data for NMR structures. wwPDB partners have also recently published papers that describe resources available from the RCSB PDB1, PDBe2, and PDBj3.

1 The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Res. (2010) doi: 10.1093/nar/gkq1021
2 PDBe: Protein Data Bank in Europe Nucleic Acids Res. (2010); doi: 10.1093/nar/gkq985
3 PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan Database (2010) doi: 10.1093/database/baq021

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21 December, 2010

Advanced Notification

From January 14, 2011, the wwPDB will resume the practice of providing advance notification of PDB entries that are about to be released. A list of the PDB ID codes that will be released in the following week will be posted at the URL http://www.wwpdb.org/pdb_codes_next_release.txt before 17:00 UTC every Friday.

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16 December, 2010

Advisory Committee Meeting

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.

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05 October, 2010

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

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

These data must be deposited at a member site of the Worldwide Protein Data Bank: BMRB, PDBj-BMRB, PDBe, RCSB PDB, or PDBj. 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 NMR Task Force, and has been endorsed by the wwPDB Advisory Committee.

Changes to wwPDB Deposition Systems

New versions of the ADIT-NMR deposition system (BMRB and PDBj-BMRB) and AutoDep (PDBe) have been developed to support the new chemical shift deposition requirement. These systems will support the deposition of chemical shift data in NMR-STAR (V3.1) format and will perform checks to confirm the correspondence between the atom nomenclature in the chemical shift and coordinate data files. AutoDep (PDBe) will also accept depositions containing chemical shifts from CCPN projects. Additional tools are provided to assist depositors in preparing and pre-checking chemical shift data prior to deposition: various data validation services are available at BMRB and PDBj-BMRB (http://www.bmrb.wisc.edu/validate/ or http://bmrb.protein.osaka-u.ac.jp/validate/) and at PDBe including the FormatConverter (http://www.ebi.ac.uk/pdbe-apps/nmr/software/formatConverter.html) and standalone tools to generate deposition ready CCPN projects from more conventional data.

Changes to wwPDB FTP Server

NMR chemical shift data files will be added to the wwPDB ftp site with each weekly release. Chemical shift data files will be named "1abc_cs.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All chemical shift data files will be compressed (.gz) using the GNU gzip program. Chemical shift files will be stored in a new directory path, grouped by the middle two characters of the 4-character PDB ID:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/. All of these data files will be symbolically linked to a single directory:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_chemical_shifts/.

In addition, the chemical shift data will be processed and included as entries in the BMRB archive.

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

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12 August, 2010

Upcoming Meeting: PDB Symposium at ACS

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).

Symposium presenters will explore all aspects of the chemical components found in the PDB archive:

  • wwPDB: An organization that provides macromolecular structural data to the global community (Helen M. Berman, RCSB PDB)
  • The wwPDB Common Annotation and Deposition Tool project (Martha Quesada, RCSB PDB)
  • Small molecule resources and search tools at the PDB (John Westbrook and Dimitris Dimitropolos, RCSB PDB)
  • Remediation of PDB entries containing molecules with antibiotic and inhibitory pharmacological properties (Kim Henrick, PDBe)
  • The synergies of the PDB and the CSD (Tjelvar S.G. Olsson, CCDC)
  • Iridium: prepping PDB data for use in computation chemistry software development (Greg Warren, OpenEye)
  • Challenges in positioning, validation, annotation and visualization of chemical compounds bound to proteins (Ruben Abagyan, UCSD)
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06 August, 2010

Validation Report PDFs

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.

As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site (Example reports: RCSB PDB | PDBe | PDBj). 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.

PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process and are described in an editorial recently published in Nature Structural & Molecular Biology.

Questions about these reports and the annotation process may be sent to info@wwpdb.org.

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13 July, 2010

RSS Feed for wwPDB News

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.

The wwPDB News Feed can be accessed by selecting the icon in the top menu bar.

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01 July, 2010

Version 2 NMR Restraint Files Available from the wwPDB FTP

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. 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.

For detailed information, please see wwPDB News: Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010.

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30 April, 2010

wwPDB To Provide Validation Reports as PDFs

As part of the structure annotation process, www.wwpdb.org 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.

As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process (see Baker et al. (2010) Acta Cryst. F66: 112). The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site. 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.

Questions about these reports and the annotation process may be sent to info@wwpdb.org.

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30 April, 2010

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

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.

About Version 2 Restraint Files

The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen.

NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos (BMRB; and CMBI/IMM), FormatConverter and NMRStarExport (PDBe), and the CCPN framework.

The complexity of this process may have lead to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data.

More information about the process used to generate these files is available (1-3).

Changes to wwPDB FTP Server

The initial release of the Version 2 NMR restraint files will add approximately 5625 new files (310 Mbytes) to the wwPDB FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly.

NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.

Version 2 restraint files will be stored in a new directory path, grouped by the middle two characters of the 4-character PDB ID:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/

All of these data files will be symbolically linked to a single directory:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_restraints_v2/

Version 1 restraint files will remain in their current directory structure.

For questions, please contact info@wwpdb.org.

References
  1. JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12.
  2. WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL Markley, J Ionides, and ED Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-696.
  3. JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389�396.
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18 February, 2010

Changes to the wwPDB Policy for Depositing Polypeptide Structures

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.

Consistent with earlier policy, depositions of polynucleotide and polysaccharide structures of 4 or more residues are also accepted. For more information, see the wwPDB Policy Guide at Annotation Documentation.

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02 February, 2010

wwPDB FTP Advisory Notice

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).

Currently, the release date reflected in the initial REVDAT record in a PDB file is marked as a Tuesday date. This release date will be changed to mirror the Wednesday release as of March 31, 2010. The file's timestamp of the Friday before release will not be changed.

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28 January, 2010

Advisory Committee Meeting

The Worldwide Protein Data Bank Advisory Committee (wwPDBAC) met in Osaka, Japan on November 6, 2009. The presentations by wwPDB members and the report from the wwPDBAC are available wwPDB Advisory Committee Meetings.

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