Protein Data Bank in Europe : Latest News

The PDBe will retire the OCA in July 2010

March 2010

The PDBe will cease hosting the OCA search system in July 2010. Users should direct links to the OCA site at the weizmann institute after this date.

Changes to the wwPDB Policy for Depositing Polypeptide Structures

February 2010

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 here

What types of structure can be deposited to the PDB? Biomolecular polymers including polypeptides, polynucleotides, polysaccharides, and their complexes that meet the following criteria are accepted:

• For polypeptide structures
1. all gene products
2. all naturally-occurring peptides that are non-ribosomal in origin
3. all peptidic repeat units of larger polymers (such as fibrous and amyloid polymers)
4. Non-naturally occurring synthetic peptides with at least 24 residues within a polymer chain
• Polynucleotide structures of four or more residues
• Polysaccharide structures of four or more residues

Crystal structures of peptides with fewer than 24 residues within any polymer chain that do not meet criteria 1,2, or 3 can be deposited at the Cambridge Crystallographic Data Centre (CCDC). NMR structures of such molecules can be submitted to Biological Magnetic Resonance Data Bank (BMRB) through the Small Molecule Structure Deposition (SMSdep) system. Smaller oligonucleotides (dinucleotides and trinucleotides) can be deposited at the Nucleic Acid Database (NDB).

Molecules that do not conform to these guidelines but have been previously deposited in the PDB will not be removed.

SIFTS files updated to the latest CATH release, as of 20th January 2010

20th January 2010

As of 20 January, 2010, the new release of SIFTS files, with regular weekly updates, includes secondary structure assignments and entry-level and residue-level cross references to the latest versions of UniProt, SCOP (currently version 1.75), CATH (currently version 3.3), Pfam (currently version 24.0), GO and InterPro.

SIFTS stands for "Structure integration with function, taxonomy and sequence" and is maintained at the EBI by the PDBe group in collaboration with UniProt.

More information about SIFTS can be found here. SIFTS files can be downloaded by ftp here. The information is also available in tab delimited format files here.

PDBeSite will not be available from 16th November 2009

16th November 2009

The PDBeSite service has been retired since all the functionality is found within the much more comprehensive PDBeMotif service. The PDBeSite was maintained as a static service (no increments) for the last 6 months to allow scientists to complete research. Please use the PDBeMotif service for all future ligand interaction analysis of the PDB data.

PQS will not be available from the 9th November 2009

9th November 2009

The PQS service as it has been finally phased out of production and we no loner support searches against this data. For the near future will will support PQS-Quick which allows the display of PQS data of a single entry, but please note that we have not been incrementing this data with new releases since August 2009. The PQS service was phased out due to the replacement by the more advanced (and automated) service called PISA.

The Macromolecular Structure Database (MSD) is now the Protein Data Bank in Europe (PDBe)

As of mid January 2009 the Macromolecular Structure database group (MSD) was renamed to the Protein Data Bank in Europe (PDBe) to highlight our close partnership within the wwPBD. The change to our site includes the following :

• Change in naming from MSD to PDBe
• Change of the underlying database to a new schema based on the mmCIF dictionary
• Change in every service to reflect the naming, URL and data differences
• Our home page is now "http://www.ebi.ac.uk/pdbe/"
• Our atlas pages have been completely redesigned to include far more information

We will endeavor to maintain our services without interruption during the transition but please inform us if you find problems on our new site as we make major changes to every aspect of the service. We hope to provide a much richer set of services in future from the new database structure.

We will maintain the old web resources under the PDBe name for the near future so that links are not broken and also so that users can complete ongoing research. Please note, we are only maintaining the old resources as static systems since the underlying data to these will not be updated with the latest depositions. We ask you to modify your links from your own services to reflect the changes in our name (PDBe) Please also change links into our pages from any services you maintain, though these should be caught with redirects as we progressively add these; and don't forget your bookmarks.

It may take a little while to convert every aspect of the PDBe group to PDBe and you may notice some inconsitency during a transition period. We trust that this will not effect your work in any way.

EM Map depositions to EMDB - New USA deposition site for the EMDB

Beginning 4 February 2008, electron microscopy map data may be deposited to the EM Data Bank at either of two sites: a new deposition site at RCSB in the USA, as well as the existing deposition site at EBI in Europe. EmDep2, an improved version of the web-based service for EM map deposition, has been installed at both sites.

Link to deposition at EBI/Europe:   PDBe/emdep
Link to deposition at RCSB/USA:   RCSB/emdep

For additional information see emdb documentation/

This improvement to EMDB services is the first product of a collaboration beween the European Network of Excellence 3D-EM (http://www.3dem-noe.org/) and the recently NIH-funded partnership for a Unified Data Resource for CryoEM (http://emdatabank.org) between the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics at Rutgers, and the National Center for Macromolecular Imaging at Baylor.

Announcement: Data Processing Procedures

Starting August 1, 2007, data depositions processed by the wwPDB will follow the PDB Exchange Dictionary (PDBx) v1.037 and the Protein Data Bank Contents Guide Version 3.1.

Files processed and released into the archive by the wwPDB sites will reflect the new features incorporated as part of the remediation project, including standardized IUPAC nomenclature for all chemical components.

Please see http://www.wwpdb.org for more details.

Testing of Remediated PDB Data - 14th May 2007

The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files.

These files are available for community testing in a variety of ways, including:
* Sets of Example Files. Sets of structures are available for download in PDB, mmCIF and PDBML formats. These sets each include ten structures that illustrate the nomenclature changes typical of the revised dictionary. Three sets are currently available: proteins, nucleic acids, and viruses.
* Chemical Component Dictionary. To review the remediated Chemical Component Dictionary, users can search or browse the dictionary by ID. Each chemical component has a summary page that provides diagrams, information on the physical and chemical features of the ligand, status information, and links to the component definition in CIF and PDBML/XML formats along with model coordinates, idealized coordinates, and chemical diagrams. The entire dictionary can also be downloaded.
* Search by PDB ID.
or navigate the FTP site,
or enter the PDB ID at PDBj

Instructions for accessing the entire archive are at download Instructions. New options for accessing these data will be announced on this site in the near future.

The entire PDB archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards.

Questions or comments about the remediation project should be sent to info@wwpdb.org.

Helen Berman, RCSB; Kim Henrick, EBI; Haruki Nakamura, PDBj; John L. Markley BMRB

16-April-2007 - Release of Remediated PDB Data

The wwPDB (www.wwpdb.org) has collaborated on a project to remediate the PDB archive and create a new set of corrected files.

The entire archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards.

A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http://www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with the current production site at ftp://ftp.rcsb.org. Both sites share the same organizational structure.

Your input is very important to us. PDB users are encouraged to test the remediated data files between April and July 2007. The final transition date will be announced on this website.

Detailed information about this project can be found at http://remediation.wwpdb.org.

Comments about the files should be sent to info@wwpdb.org. Major announcements will be made at the wwPDB website (http://www.wwpdb.org) as well as on the individual member websites.

3DEM Image Conventions

1st December 2005 - Testing Images and Image Rotations for Compliance with 3DEM Image Conventions

Following on from a recent workshop held at the EBI, with participation from the European NOE in 3DEM and with developers from the United States, it was recognised that data standards are of crucial importance. A set of 3DEM Image Conventions was agreed upon and now a description of the recommended 3DEM Images Conventions, by David Belnap, is available. more....

3DEM Data Exchange

19th January 2005 - 3DEM Data Exchange Conventions Draft Document

Three-dimensional electron microscopy (3DEM) has made an important contribution to strucutral biology. The independent development of algorithms and software packages, together with map conventions, has reflected the individualistic approach to 3DEM. Now, in an era where information exchange is important the standardising of conventions is of crucial importance. In order to address these issues a paper on the 'Common Conventions for Interchange and Archiving of Three-Dimensional Electron Microscopy Information in Structural Biology', by J.B.Heymann, M.Chagoyen and D.M.Belnap, is available, see details here.

BIObar Enhanced

1st December 2003 - BIObar Enhanced

BIObar - A toolbar application to search the MSD, RCSB, PDB Japan and OCA data collections.

BIObar is a Netscape/Mozilla toolbar application for searching the PDBe and other macromolecular structure resources.

The toolbar takes a few seconds to install and can be used to search the MSD, RCSB, PDBj or OCA directly from the browser, thereby providing quick access for simple searches.

The latest version of BIObar (Version 0.5) has the following features among others:

1. Search using MSD, RCSB, PDBj or OCA search systems.
2. Choice of RCSB and OCA mirrors for faster searching.
3. Download detailed information for individual PDB IDcodes.
4. Search data collections by Author, Keyword, Ligand, Source etc.
5. Browse EDS summary for given PDB IDcode (External Link to EDS).
6. Compare 3-D protein structures using MSDfold using default parameters.
7. Search PubMed at the NCBI for simple author/subject searches.

BIObar has been tested on Netscape 6.0+ as well as on Mozilla 1.3 and above on many different platforms.

For more information and download/installation details, please visit BIObar

PDBe Search Documentation

June 2003 - PDBe search database documentation

Reference documentation of the public PDBe search database:

The PDBe search relational database is derived from the PDB and has the aim of providing a knowledge discovery and data mining environment for biological structure data.

A document describing the data base contents is now available: see documentation

These pages provide in depth, detailed documentation aiming to explain the structure of the public PDBe search database to the serious developer or researcher that wishes to use its capabilities in full.

The database is now under test for distribution and weekly update procedures with our partner sites and is expected to be made available for general distribution in mid-November 2003.

Secondary Structure Matching

May 2003 - SSM service now available for download

PDBe Protein Structure Comparison service SSM PDBeFold

is now available for download and in-house installation under both academic (free) and commercial licenses at

http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmdcenter

The installed SSM may be used as a local web-server or a standalone application, running on one or several parallel CPUs, able to serve multiple queries simultaneously. SSM may communicate with user's applications through XML.