wwPDB 2014 News
Contents
09/18/2014
Inclusion of Large Structures in the Main PDB Archive
The wwPDB recently combined entries that represent large structures (such as ribosomes) across multiple PDB files (SPLIT entries) into single files. These combined structures have been issued new PDB IDs and are represented in the archive in both PDBx/mmCIF and PDBML formats. As announced previously, these files were made available in a separate FTP directory for public testing.
These combined entries will be fully integrated into the main PDB FTP archive on December 10, 2014 as part of the regular weekly update. The corresponding "SPLIT"entries will be removed (obsoleted). Users searching for ID codes of "SPLIT" entries at wwPDB member websites will be automatically redirected to the combined entry.
As part of the same update, a separate directory in the PDB FTP archive will contain a tar file including a collection of "best-effort," limited PDB-format files for large structures that contain authorship, citation details and coordinate data and a mapping file that contains the mapping between the chains present in the the large entry and the chains present in the limited PDB-format files.
After December 10, 2014, large structures (>62 chains and/or 99999 ATOM lines) will only be distributed in the main PDB FTP directory in PDBx/mmCIF and PDBML formats. Structures that do not exceed the limitations of the PDB format will continue to be provided as PDB files in the archive for the foreseeable future.
Main PDB FTP archive for PDB structures.
Single files representing large structures will be integrated into this directory on December 10, 2014.
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ (wwPDB/RCSB PDB)
ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/ (PDBe)
ftp://ftp.pdbj.org/pub/pdb/data/structures/ (PDBj)
Obsolete directory
"SPLIT" entries corresponding to large structures will be moved to this directory on December 10, 2014.
ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/ (wwPDB/RCSB PDB)
ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/obsolete (PDBe)
ftp://ftp.pdbj.org/pub/pdb/data/structures/obsolete/ (PDBj)
New directory for PDB format-like files for large structures
Location of collected "best-effort" PDB-format files begining December 10, 2014.
ftp://ftp.wwpdb.org/pub/pdb/compatible/pdb_bundle (wwPDB/RCSB PDB)
ftp://ftp.ebi.ac.uk/pub/databases/pdb/compatible/pdb_bundle (PDBe)
ftp://ftp.pdbj.org/pub/pdb/compatible/pdb_bundle (PDBj)
Email [email protected] to contact the wwPDB.
08/01/2014
wwPDB Events at IUCr (August 5-12)
Meet wwPDB members from around the globe at the 23rd General Assembly and Congress of the International Union of Crystallography (IUCr, August 5-12, 2014) in Montreal, Quebec, Canada.
Come to exhibition stand 114 to receive a special sticker celebrating your contributions to the 100,000+ structures in the PDB archive.
Other wwPDB events include:
Thursday August 7
- Poster: The New wwPDB Deposition and Annotation System presented by John Westbrook (RCSB PDB) BM.P54.A536
Saturday August 9
- Oral Presentation: The history of the PDB as a public resource for enabling science by Helen M. Berman (RCSB PDB) in MS61 The Beginnings Of Biological Crystallography (1:45 - 4:20pm) in Room 517d.
- Poster: Educational Outreach and User Training at the Worldwide Protein Data Bank (MS84.P01.B415) presented by Matthew Conroy (PDBe) and Christine Zardecki (RCSB PDB).
- Poster: Japanese Science & Technology with Crystallography (MS86.P17.B445) presented by Atsushi Nakagawa (PDBj).
Monday August 10
- Oral Presentation: Educational Outreach and User Training at the Worldwide Protein Data Bank (MS84.P01.B415) by Matthew Conroy (PDBe) and Christine Zardecki (RCSB PDB) in MS84 Crystallography Education and Training in the 21st Century: New Pedagogies, New Paradigms, Part I (9:40am-12:15pm) in room 517a.
Tuesday August 12
- Oral Presentation: New wwPDB validation pipelines for X-ray, NMR and 3DEM structures by Sameer Velankar (PDBe) in MS100 Beginner's Guide to Validation of Crystallographic Results on (9:40am - 12:15pm) in room 517a.
06/27/2014
Improved Representation of Large Structures in the PDB Archive
To meet the challenges of greater numbers of PDB depositions,
involving ever larger and more complex structures, often determined
using multiple methods, wwPDB has developed a new software system for
structure deposition and annotation. This new system, currently in
production for X-ray crystallographic entries, is based on the
PDBx/mmCIF format and can thus handle structures of any size. Large
structures have been processed and released intact by wwPDB since May 2013.
As announced previously, wwPDB
has now combined the structures that were historically "split" across
multiple entries into single PDBx/mmCIF files. Each combined file has
been issued a new PDB identifier. This constitutes a significant
improvement in the representation of large entries in the PDB archive.
The combined files will be made publicly available through the PDB
archive on July 9, 2014. However, for a transition period of 6 months,
these large PDBx/mmCIF files will be available only in a separate ftp
area (see below) so they can be thoroughly reviewed and tested by the
PDB user community. During this transition period, the original
"split" PDB-format files will remain available from the active
archive. The relationship between the split and combined entries will
be described in the combined PDBx/mmCIF file in the item
pdbx_database_related.
After the transition period, the combined PDBx/mmCIF files will be
moved from the separate large_structures directory into the main PDB
FTP archive. At that time, the multiple "split" entries will be taken
out of the active archive, and searches of the archive at all wwPDB
member sites using the PDB identifier of a split entry will return the
new "combined" entry that represents the full structure.
Developers and users should note that after the transition period,
PDBx/mmCIF will be the definitive format used for archive
distribution. Due to the limitations of the old PDB format it cannot
be used to represent large structures and therefore PDB files will
only be provided on a best-effort basis, outside of the active
archive. Developers and users who process the entire archive should
therefore make sure that their software supports PDBx/mmCIF towards
the end of 2014. Resources for this are described at http://mmcif.wwpdb.org.
The wwPDB has convened a Working Group for PDBx/mmCIF Data Deposition, chaired by Paul Adams, that includes
representatives from the major providers of X-ray structure-refinement
software. To ease the transition from the PDB file format to
PDBx/mmCIF, the Working Group has made recommendations about essential
format extensions required for large structures that have been used in
creating the consolidated data files. These include:
- Atom serial numbers will run from 1 to the number of atoms (with
no field-width restrictions);
- Chain identifiers of up to 4 characters will be accepted.
- Cartesian coordinates will have field widths as large as required
(and maintain their current precision of 3 decimal places);
- Isotropic B-factors and occupancies will be represented with 3
decimal places precision.
PDBx/mmCIF files suitable for deposition can be created with recent
versions of the CCP4 (REFMAC 5.8) and Phenix (1.8.2) software
packages. Both packages support the above extensions for large
structures.
Users and developers with questions about the new deposition system or
the procedures for handling large structures should contact [email protected].
During the transition period, the combined large-structure files
will be available from:
- ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/ (wwPDB/RCSB
PDB)
- ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/large_structures/
(PDBe)
- ftp://ftp.pdbj.org/pub/pdb/data/large_structures/ (PDBj)
05/13/2014
PDB Reaches a New Milestone: 100,000+ Entries
In the weeks leading up to this historic event, wwPDB has looked
back at other PDB milestones. (Previously: Building a Community Resource, The Early Structures, Launching Tools for the Next Generation)
Depositors: Download this image and write the number of structures
deposited.
With this week's update, the PDB archive contains a record 100,147
entries.
Established in 1971, this central, public archive has reached this
critical milestone thanks to the efforts of structural biologists
throughout the world who contribute their experimentally-determined
protein and nucleic acid structure data.
Four wwPDB data centers support online access to three-dimensional
structures of biological macromolecules that help researchers
understand many facets of biomedicine, agriculture, and ecology, from
protein synthesis to health and disease to biological energy. The
archive is quite large, containing more than 1,000,000 files related
to these PDB entries that require more than 249 GBbytes of storage.
Function follows form
In the 1950s, scientists had their first direct look at the
structures of proteins and DNA at the atomic level. Determination of
these early three-dimensional structures by X-ray crystallography
ushered in a new era in biology-one driven by the intimate link
between form and biological function. As the value of archiving and
sharing these data were quickly recognized by the scientific
community, the Protein Data Bank (PDB) was established as the first
open access digital resource in all of biology by an international
collaboration in 1971 with data centers located in the US and the UK.
Among the first structures deposited in the PDB were those of
myoglobin and hemoglobin, two oxygen-binding molecules whose
structures were elucidated by Chemistry Nobel Laureates John Kendrew
and Max Perutz. With this week's regular update, the PDB welcomes 219
new structures into the archive. These structures join others vital to
drug discovery, bioinformatics and education.
The PDB is growing rapidly, doubling in size since 2008, and
releasing around 200 new structures to the scientific community every
week. The resource is accessed hundreds of millions of times annually
by researchers, students, and educators intent on exploring how
different proteins are related to one another, to clarify fundamental
biological mechanisms and discover new medicines.
"The PDB is a critical resource for the international community
of working scientists which includes everyone from geneticists to
pharmaceutical companies interested in drug targets," said Nobel
laureate Venki Ramakrishnan of the MRC Laboratory of Molecular Biology
in Cambridge, UK.
A growing community
Since its inception, the PDB has been a community-driven enterprise,
evolving into a mission critical international resource for biological
research. Since 2003 the Worldwide PDB (wwPDB) organization, a
collaboration involving four PDB data centers in the US, UK, and
Japan, has ensured that these valuable data are securely stored,
expertly managed, and made freely available for the benefit of
scientists and educators around the globe. wwPDB data centers work
closely with community experts to define deposition and annotation
policies, resolve data representation issues, and implement community
validation standards. In addition, the wwPDB works to raise the
profile of structural biology with increasingly broad audiences.
Each structure submitted to the archive is carefully curated by
wwPDB staff before release. New depositions are checked and enhanced
with value-added annotations and linked with other important
biological data to ensure that PDB structures are discoverable and
interpretable by users with a wide range of backgrounds and interests.
Future challenges
The scientific community eagerly awaits the next 100,000 structures
and the invaluable knowledge these new data will bring. However, the
increasing number, size and complexity of biological data being
deposited in the PDB and the emergence of hybrid structure
determination methods, which use a variety of biophysical,
biochemical, and modelling techniques to determine the shapes of
biologically relevant molecules, constitute major challenges for the
management and representation of structural data. wwPDB will continue
to work with the community to meet these challenges and ensure that
the archive maintains the highest possible standards of quality,
integrity, and consistency.
Email [email protected] to contact
the wwPDB.
05/06/2014
The Road to 100,000 Entries: Launching Tools for the Next Generation
With this week's update, the PDB archive contains 99,928
entries and will soon pass the milestone of 100,000. In the weeks
leading up to this event, wwPDB is looking back at other PDB
milestones. (Previously: Building a Community Resource and The Early Structures)
Many structures deposited to the PDB today require special tools and
processes for data capture and annotation in order to ensure the best
representation in the archive. To meet the challenges posed by large
structures, complex chemistry, and use of multiple experimental
methods, the wwPDB is launching a new Deposition and Annotation System that will allow the partners to
meet the evolving needs of the scientific community over the next
decade.
Since its initial launch at the end of January, >750 X-ray
crystallographic structures from 30 countries have already been
deposited using the new system.
For data depositors, new or enhanced features include the generation
of X-ray validation reports (following
the recommendations of the wwPDB X-ray Validation Task Force), improved capture and review of ligand
information, the ability to replace coordinate and/or experimental
data files pre- and post-submission, improved communication process
between depositors and wwPDB curators, and the ability to preview and
download the PDBx/mmCIF entry file prior to submission.
For data users, the new annotation system greatly improves the
efficiency and consistency of data processing.
The system will replace all current deposition and annotation
systems in use at the wwPDB deposition centers.
Deposit data with the new system at http://deposit.wwpdb.org/deposition/.
04/29/2014
The Road to 100,000 Entries: The Early Structures
With this week's update, the PDB archive contains 99,775 entries
and will soon pass the milestone of 100,000. In the weeks leading up
to this event, wwPDB is looking back at other PDB milestones.
Scientists first began to decipher the 3D structure of proteins at the
level of individual atoms using X-ray crystallography in the 1950s.
These views of the structures of myoglobin,1,
2 hemoglobin,3
lysozyme,4,
5 and ribonuclease
6,
7
provided unexpected insights into the regularities and similarities of
proteins, and relationships between sequence, structure and function,
and evolution. The enormous potential for scientific discovery and
understanding was recognized early and rewarded with several Nobel
prizes.8 These early structures
also inspired a new field of scientific endeavor: molecular structural
biology.
The cover of the wwPDB's 2014 calendar highlights the first entries deposited to the PDB
archive.
Beginning with just seven entries-carboxypeptidase, chymotrypsin,
cytochrome, hemoglobin (lamprey), lactate dehydrogenase, subtilisin,
and trypsin inhibitor9-15-the PDB
archive was established in 1971 to provide both a home and an access
point to these information-rich structures. It is a testament to the
vision and foresight of the pioneers in the field that they understood
the value and potential of archiving and sharing data in an era when
computer networking was virtually non-existent.
Since its inception, the size of the archive has increased by a
factor of 10 roughly every 10-15 years: the PDB reached 100 released
entries in 1982, 1000 entries in 1993, and 10,000 in the year 2000.
When the 100,000th is made available in May 2014, ~90% of the archive
will have been released in the past fourteen years.
For a look at some of the milestone entries in the archive, see PDB
Pioneers at RCSB PDB's Molecule of the Month; Biophysical Highlights from 54 Years of
Macromolecular Crystallography in Biophysical Journal, Revealing Views of Structural Biology in Biopolymers;
and A brief history of macromolecular crystallography,
illustrated by a family tree and its Nobel fruits in FEBS
Journal.
PDB structures are also regularly highlighted in PDBe's Quite Interesting
PDB Structures (Quips) features; PDBj's Encyclopedia
of Protein Structures (eProtS), and the Molecule
of the Month series at RCSB PDB (also available in
Japanese at PDBj).
Dickerson, B. E. Strandberg, et al. (1960) Structure of myoglobin: A
three-dimensional Fourier synthesis at 2 A. resolution. Nature
185: 422-427.
M. Dintzis, et al. (1958) A three-dimensional model of the myoglobin
molecule obtained by x-ray analysis. Nature 181: 662-666.
Rossmann, A. F. Cullis, et al. (1960) Structure of haemoglobin: a
three-dimensional Fourier synthesis at 5.5 Å resolution,
obtained by X-ray analysis. Nature 185: 416-422.
Johnson, G. A. Mair, et al. (1967) Crystallographic studies of the
activity of hen egg-white lysozyme. Proc. R. Soc. London Ser. B
167: 378-388.
Koenig, G. A. Mair, et al. (1965) Structure of hen egg-white
lysozyme. A three dimensional Fourier synthesis at 2 Å
resolution. Nature 206: 757-761.
Harker. (1967) Tertiary structure of ribonuclease. Nature 213:
862-865.
Hardman, N. M. Allewell, et al. (1967) The structure of
ribonuclease-S at 6 Å resolution. J. Biol. Chem. 242:
3749-3753.
Wlodawer. (2014) A brief history of macromolecular crystallography,
illustrated by a family tree and its Nobel fruits. FEBS Journal
in press.
Lipscomb. (1986) X-ray crystallographic investigation of substrate
binding to carboxypeptidase A at subzero temperature. Proc Natl
Acad Sci U S A 83: 7568-7572.
Blow. (1972) Structure of crystalline alpha-chymotrypsin. V. The
atomic structure of tosyl-alpha-chymotrypsin at 2 Å resolution.
J Mol Biol 68: 187-240.
Mathews. (1996) Refinement and structural analysis of bovine
cytochrome b5 at 1.5 A resolution. Acta Crystallogr D Biol
Crystallogr 52: 65-76.
Love, J. Karle. (1973) Crystal structure analysis of sea lamprey
hemoglobin at 2 Å resolution. J Mol Biol 74: 331-361.
Griffith, J. L. Sussman, et al. (1987) Refined crystal structure of
dogfish M4 apo-lactate dehydrogenase. J Mol Biol 198: 445-467.
Birktoft, J. Kraut, et al. (1971) Atomic coordinates for subtilisin
BPN' (or Novo). Biochem Biophys Res Commun 45: 337-344.
Deisenhofer, J., Bode, W., Huber, R. (1983) The geometry of the
reactive site and of the peptide groups in trypsin, trypsinogen and
its complexes with inhibitors. Acta Crystallogr B39: 480.
04/22/2014
The Road to 100,000 Entries: Building a Community Resource
With this week's update, the PDB archive contains
99,624 entries and will soon pass the milestone of 100,000. In the
weeks leading up to this event, wwPDB is looking back at other PDB
milestones.
Through lively conversations, debates, and planning for the future, a
community of structural biologists banded together to establish the
PDB in 1971 at Brookhaven National Laboratory1
as an archive for the experimentally-determined 3D structures of
biological macromolecules. Today, the PDB archive is managed by the
Worldwide Protein Data Bank,2 a
unique collaboration of organizations that act as deposition, curation
and distribution centers for PDB data.3
The wwPDB's mission is to maintain a single PDB archive of
macromolecular structural data that is freely and publicly available
to the global community.4,5
In support of this mission, wwPDB works closely with the various
communities that rely on the archive. wwPDB has convened Task Forces
for X-ray, NMR,
3DEM and Small Angle Scattering that bring together acknowledged experts in
these fields to advise wwPDB on issues of method-specific validation,
deposition and annotation. Their recommendations are implemented in
wwPDB validation pipelines that are an integral part of the new Deposition and
Annotation system.
Validation reports produced by this pipeline have recently been released for all X-ray structures in the current archive; reports for NMR and EM
structures will follow later.
Through a dedicated PDBx/mmCIF Working Group, wwPDB works with software developers from the major
macromolecular crystallographic software packages on the
representation of large structures, complex chemistry, and new and
hybrid experimental methods in the PDB. Recommendations about
essential extensions to PDBx/mmCIF have been developed to accommodate
large structures, and CCP4 and Phenix can now produce PDBx/mmCIF files
suitable for deposition.
An international advisory committee,
made up of experts in X-ray crystallography, 3DEM, NMR, and
bioinformatics, advises the wwPDB and meets annually.
Members of the PDB, past and present, in attendance at PDB40.
(Photo by Constance Brukin)
In addition, wwPDB reaches out to the wider community through symposia
and publications. One notable event was the
2011 symposium celebrating the 40th anniversary of the Protein Data Bank (PDB40) held at Cold
Spring Harbor Laboratory, the intellectual birthplace of the PDB. Many
distinguished speakers described structural biology's past, present
and future. Selected presentations from this event are available online.
Recently, the wwPDB created a 2014 calendar in celebration of the International Year of
Crystallography. This calendar is available for download in PDF and PowerPoint
formats.
Many publications describe the development and future of the PDB
archive and wwPDB organization, including: How community has shaped
the Protein Data Bank (Structure, 2013),
The future of the Protein Data Bank (Biopolymers,
2013), and Creating a Community Resource for Protein Science (Protein
Science, 2012). A full list is available.
1. Protein Data Bank. (1971) Protein Data Bank.
Nature New Biol. 233: 223.
2. H. M. Berman, K. Henrick, H. Nakamura. (2003) Announcing the worldwide Protein Data Bank.
Nat Struct Biol 10: 980.
3. H. M. Berman, G. J. Kleywegt, H. Nakamura, J.L. Markley (2013) The future of the protein data bank.
Biopolymers 99: 218-222.
4. H. M. Berman, G. J. Kleywegt, H. Nakamura, J.L. Markley (2013) How community has shaped the Protein Data Bank.
Structure 21: 1485-1491.
5. H. M. Berman, G. J. Kleywegt, H. Nakamura, J.L. Markley (2012) The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future.
Structure 20: 391-396.
03/18/2014
wwPDB X-ray validation reports added to PDB archive
Validation reports for all X-ray crystal structures released in the
PDB archive are now publicly available.
The reports are accessible from the following FTP sites:
The reports were added to the FTP archives as part of the March 19,
2014 update, adding ~56 GB of data. Files are organized in directories
following the 2-character hash code format. For example, files for
entry 1ABC will be found in directory
/pdb/validation_reports/ab/1abc/. All files are compressed using gzip
(http://www.gzip.org/) compression.
Five files will be included in the directory for each entry:
- Standard wwPDB validation report as a PDF file (e.g.,
1abc_validation.pdf.gz)
- Validation report containing all outliers as a PDF file (e.g.,
1abc_full_validation.pdf.gz)
- Summary quality graphic as a PNG image (e.g.,
1abc_multipercentile_validation.png.gz)
- Summary quality graphic as a SVG image (e.g.,
1abc_multipercentile_validation.svg.gz)
- Data file containing all diagnostics in machine-readable XML
format (e.g., 1abc_validation.xml.gz)
Instructions for downloading data from the PDB archive are available.
The validation reports contain an assessment of the quality of a
structure and highlight specific concerns by considering the
coordinates of the model, the experimental data and the fit between
the two. Easily interpretable summary information that compares the
quality of a model with that of other models in the archive will help
users of PDB data to critically assess archived entries and to select
the most appropriate structural models for their needs.
The reports implement recommendations of a large group of community experts on validation of X-ray
crystal structures and have been developed in the context of a larger
initiative, the new wwPDB Deposition and Annotation system, which was created to
unify the annotation tools and practices used across all wwPDB
deposition centers and for all common structure-determination methods.
The new X-ray structure-validation reports have been provided to
depositors as part of the structure-annotation process since August 2013. More
recently, a stand-alone wwPDB X-ray structure validation server was launched allowing
crystallographers to generate reports on demand in order to check
early, intermediate and near-final models and to help them to identify
any potential problems that need addressing prior to structure
analysis, publication and deposition.
Further information, including sample X-ray validation reports, is available. We
welcome your feedback on the new validation reports. If you would like
to send us your comments or questions, then please contact [email protected].
01/31/2014
Archiving Structures Derived from SAS Data
Small-angle scattering (SAS) methods are increasingly used to study
the 3D structure of biomacromolecules, either by themselves or in
conjunction with other techniques (e.g., crystallography, NMR, 3DEM).
The wwPDB has convened an SAS Task Force
made up of experts in X-ray and neutron scattering, as well as experts
in crystallography, NMR, 3DEM, modeling and archiving.
The Task Force had its inaugural meeting in 2012, where it considered
whether the archiving of SAS-based models would be of value to the
structural biology community and, if so, what kinds of experimental
data, meta-data and validation methods would be required. A report
summarizing the Task Force recommendations was published in the
journal Structure (Trewhella et al., 21, 875-881 (2013)). The Task
Force strongly recommended that a global archive for SAS data and
purely SAS-derived models be established, separate from (but federated
with) the PDB archive.
There are a few dozen models in the current PDB archive that are
based solely on SAS data. The Task Force recommends that these models
are also transferred to the future SAS data and model archive, and at
that stage be removed from the active PDB archive.
The Task Force also recommended that the models based solely on SAS
data previously submitted to the PDB that are currently on-hold
awaiting a policy decision should not be processed or archived in the
PDB. Instead, they should be transferred to and processed by the
future SAS data and model archive once this has been established. The
wwPDB will follow this recommendation, and in addition, apply this to
any similar structures deposited to the PDB archive. These SAS entries
will be issued a PDB ID code, but not processed or released.
Questions may be sent to [email protected].
01/27/2014
New wwPDB Deposition System Now Available for X-ray Structures
The wwPDB partners are pleased to announce the launch of a new
deposition system for structures determined using X-ray
crystallography. The deposition system can be accessed at http://deposit.wwpdb.org/deposition/.
The new system was developed to allow the wwPDB partners to meet the
evolving needs of the scientific community over the next decade,
including support for very large systems, complex chemistry, and joint
use of multiple experimental methods. The system replaces all current
deposition and annotation systems in use at the wwPDB deposition
centers, and will lead to improved efficiency and consistency.
New or enhanced features of the deposition system include the
generation of X-ray validation reports (following the recommendations
of the wwPDB X-ray Validation Task Force), improved capture and review
of ligand information, the ability to replace coordinate and/or
experimental data files pre- and post-submission, improved
communication process between depositors and wwPDB curators, and the
ability to preview and download the PDBx/mmCIF entry file prior to
submission.
Depositors will have the option to use the new system or one of the
legacy deposition tools (ADIT, AutoDep) for most of 2014. After the
transition to the new system, the legacy tools will be available for a
limited period of time to complete any unfinished deposition sessions.
In the interest of a smooth transition, the number of X-ray
structures that will be processed by the new system will increase
gradually over the next few months. After this period, it will also
become possible to deposit NMR and 3DEM structures with the new
system.
Up-to-date information about the new system is available at here.
Webinars to demonstrate the new system will be announced in the near
future.
01/16/2014
Coming soon: X-ray Validation Reports for Archived PDB Structures
The wwPDB partners are pleased to announce that validation reports
for all X-ray crystal structures already in the PDB archive will be
made publicly available in February.
These validation reports assess the quality of a structure and
highlight specific concerns by considering the coordinates of the
model, the experimental data and the fit between the two. Easily
interpretable summary information that compares the quality of a model
with that of other models in the archive will help users of PDB data
to critically assess archived entries and to select the most
appropriate structural models for their needs.
The reports implement recommendations of a large group of community experts on validation and have
been developed in the context of a larger initiative, the new wwPDB Deposition and Annotation System,
which was created to unify the annotation tools and practices used
across all wwPDB deposition centres and for all common
structure-determination methods.
Since August 2013 the new
X-ray structure-validation reports have been provided to depositors as
part of the structure-annotation process. More recently, a stand-alone wwPDB X-ray
structure validation server was launched allowing
crystallographers to generate reports on demand in order to check
early, intermediate and near-final models and to help them to identify
any potential problems that need addressing prior to structure
analysis, publication and deposition.
Further information, including sample X-ray validation reports, is available. We welcome
your feedback on the new validation reports. If you would like to send
us your comments or questions, then please contact [email protected]
01/08/2014
wwPDB Partners Prepare to Launch New Deposition System
The wwPDB partners are pleased to announce that the new deposition
system will be released at the end of January 2014 for structures
determined using X-ray crystallography. The new web-based deposition
tool combines many features of the existing deposition systems with
enhanced data visualization and contextual communication with wwPDB
data curators.
The deposition interface is a key part of the new wwPDB Deposition
and Annotation System, which was created to unify the deposition and
annotation tools and practices across all wwPDB deposition centers.
Several structures have already been deposited, annotated, and
released using this new system, which has been in beta testing since
the summer. The new system will support all experimental methods
currently archived by the wwPDB, with deposition tools for NMR and
3DEM made available later in 2014.
Depositors will have the option to use the new system or one of the
legacy deposition tools (ADIT, AutoDep) through the end of 2014. At
that time, the legacy tools will stop accepting new entries, and will
only be available for a limited period of time to complete in-progress
deposition sessions.
Information about the new system is available, and updated regularly. Webinar
demonstrations will be announced in the near future.
01/08/2014
Announcement: Standardization of Amino Acid Nomenclature
The wwPDB is transitioning to use the nomenclature for pyrrolysine
and selenocysteine as recommended by the joint nomenclature committee
of IUPAC/IUBMB.
Starting in January, PYL (for pyrrolysine) and SEC (for
selenocysteine) will be used where three-letter codes appear for amino
acids in new releases and updated in entries currently in the archive
(<50 entries).
In April, the letter O (for pyrrolysine) and U (for selenocysteine)
will be used where one-letter codes appear for amino acids in new
releases and updated in entries currently in the archive.
Questions and comments should be sent to [email protected].
01/08/2014
Time-stamped Copies of the PDB Archive
A snapshot of the PDB archive (
ftp://ftp.wwpdb.org) as of January 2, 2014 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 20140102 includes the 96,692 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.
01/02/2014
Download the wwPDB calendar for IYCr:2014
2014 has been declared the International Year of Crystallography (IYCr2014) by the
United Nations Educational, Scientific and Cultural Organization
(UNESCO) and the International Union of Crystallography (IUCr).
IYCr2014 commemorates the centennial of X-ray diffraction and
celebrates the important role of crystallography in the modern world.
The wwPDB has created a 2014 calendar that illustrates how X-ray
crystallography enables our understanding of biology at the atomic
level.
In honor of 2014: The International Year of Crystallography, the wwPDB
has created a 2014 calendar that illustrates how X-ray crystallography
enables our understanding of biology at the atomic level. The calendar
is available for download in PDF, PPT, and individual image formats.