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The PDB is one of three core archives jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. Three wwPDB members, RCSB Protein Data Bank (RCSB PDB), Protein Data Bank in Europe (PDBe) and Protein Data Bank Japan (PDBj) share deposition, biocuration and validation responsibilities contributing to the management of this single global archive of 3D biostructure data for macromolecules. RCSB PDB also serves as the wwPDB-designated PDB Archive Keeper.
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Founded in 2003, the Worldwide Protein Data Bank (wwPDB) is dedicated to archiving, management, and public dissemination of structural biology data, and is committed to the FAIR Principles (Findability, Accessibility, Interoperability, Reusability) that are emblematic of responsible stewardship of public domain information.
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wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these extended IDs will not be supported by the legacy PDB file format. (see previous announcement)
CCD entries are currently identified by unique three-character alphanumeric IDs. At current growth rates, we anticipate running out of three-character IDs before 2024. After this point, the wwPDB will issue five-character alphanumeric accession codes for CCD IDs in the OneDep system. To avoid confusion with current four-character PDB IDs, four-character codes will not be used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes will only be distributed in PDBx/mmCIF format.
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wwPDB will be extending PDB ID length to eight characters prefixed by ‘pdb’, e.g., pdb_00001abc. Each PDB entry has a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals and described in publications by the structure authors. Extended PDB IDs and corresponding PDB DOIs have been included in the PDBx/mmCIF formatted atomic coordinate files for all new and re-released entries since August 2021.
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loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1abc pdb_00001abc 10.2210/pdb1abc/pdb
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loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB pdb_00099xyz pdb_00099xyz 10.2210/pdb_00099xyz/pdb
After all four-character PDB IDs are consumed, newly-deposited PDB entries will only be issued extended PDB ID codes, and PDB entries will only be distributed in PDBx/mmCIF format. PDB entries with four-character PDB IDs will remain unchanged.
wwPDB is asking users and software developers to review their code and remove any current limitations on PDB and CCD ID lengths, and to enable use of PDBx/mmCIF format files. Example files with extended PDB and/or CCD IDs are available via github to assist code revisions, see https://github.com/wwPDB/extended-wwPDB-identifier-examples. To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/.
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wwPDB has introduced DNS names for programmatic access to PDB archive downloads:
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Starting September 2023, wwPDB will start enforcing use of these updated DNS names. URLs in which the DNS name doesn’t match the protocol (e.g., https://ftp.wwpdb.org, ftp://files.wwpdb.org) will no longer work at that time.
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Starting September 23, wwPDB validation of 3DEM structures for which there is both a model and an EM volume will include the Q-score metric (Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations from the wwPDB/EMDB workshop on cryo-EM data management, deposition and validation in 2020 (white paper in preparation), as well as EM Validation Challenge events (Lawson C., et al., 2020, Struct. Dyn.; Lawson, et al., 2021, Nat. Methods). This will be the first quantitative parameter of residue and chain resolvability for EM maps in wwPDB validation reports and will provide an additional map-model assessment criterion.
The Q-score calculates the resolvability of atoms by measuring similarity of the map values around each atom relative to a Gaussian-like function for a well resolved atom. Q-score of 1 indicates that the similarity is perfect whilst closer to 0 indicates the similarity is low. If the atom is not well placed in the map then a negative Q-score value may be reported. Therefore, Q-score values in the reports will be in a range of -1 to +1.
The wwPDB EM validation reports will provide Q-scores for single particle, helical reconstruction, electron crystallography and subtomogram averaging entries for which both an EM map and coordinate model have been deposited.
Validation reports (PDF files) will contain images of the average per-residue Q-scores color-mapped onto ribbon models with views from three orthogonal directions. Similar images will also be introduced to visualize the per-residue atom-inclusion scores. Comparison of these two sets of images will assist in visual assessment of the model-to-map fit and quality.
The images below show the model with each residue colored according to its Q-score.
Example showing mostly cyan colors indicating Q-score closer to 1 and a good resolvability of atoms
Example showing mostly red colors indicating Q-score closer to 0 and not a good resolvability of atoms
The validation reports will also contain a table of average per-chain values of both metrics (Q-score and atom inclusion) as well as their overall average values for the entire model.
The per-residue and the per-chain average atom-inclusion and Q-score values will also be provided in the mmCIF and XML formatted validation files. The mmCIF categories _pdbx_vrpt_summary_entity_fit_to_map and _pdbx_vrpt_model_instance_map_fitting will be introduced to include both the Q-scores and atom-inclusion values. The existing items, _pdbx_vrpt_summary_entity_geometry.average_residue_inclusion and _pdbx_vrpt_model_instance_geometry.residue_inclusion for atom inclusion will no longer be used.
The PDB Core Archive holds validation reports that assess each 3DEM model in the PDB along with the associated experimental 3D volume in EMDB. Validation reports of 3DEM structures (map and model) can be downloaded at the following wwPDB mirrors:
The EMDB Core Archive holds validation reports that assess each EMDB map/tomogram entry. Validation reports for all EMDB volumes can be downloaded at the following wwPDB mirrors:
Additional information about validation reports is available for EM map+model, EM map-only, and EM tomograms.
If you have any questions or queries about wwPDB validation, please contact us at validation@mail.wwpdb.org.
[ wwPDB News ]
A new article by the wwPDB and the PDBx/mmCIF Working Group describes the community-driven data representation for structural biology data that is critical to the PDB archive. It describes file standards and governance, and summarizes software tools for data processing and checking.
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg V. Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach
(2022) Journal of Molecular Biology 434: 167599 doi: 10.1016/j.jmb.2022.167599
This article is dedicated to John D. Westbrook, whose work established the PDBx/mmCIF data dictionary and format as the foundation of the modern Protein Data Bank (PDB) archive (wwPDB.org).
[ wwPDB News ]
Starting May 3, 2022, the PDB archive distributes assembly files in PDBx/mmCIF format, allowing direct access and visualization of the curated assemblies for all PDB entries (original announcement).
Previously, PDBx/mmCIF formatted assembly files provided for structures were non-PDB compliant, however the coordinates use model numbers to differentiate alternate symmetry copies of PDB chain IDs. This method is not ideal, nor necessary, for the current archive PDBx/mmCIF format and has led to limited use of these files in community software tools. In response to this issue and recommendations by the wwPDB advisory committee, we are implementing updated, standardized practices for generation of assembly files for all PDB entries.
These updated PDBx/mmCIF format assembly files have improved organization of assembly data to support usage by the community. These files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs (_atom_site.auth_asym_id and _atom_site.label_asym_id) assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules:
In addition, entity ID and chain ID mapping categories are provided: _pdbx_entity_remapping and _pdbx_chain_remapping.
A new directory (ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/) was created for the distribution of these updated assembly files. The directory containing the existing assembly mmCIF files for large entries has been removed (ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/).
wwPDB asks all PDB users and software developers to review code and address any limitations related to PDB assemblies. Sample files were made available for testing purposes and to support community adoption at GitHub.com/wwpdb/assembly-mmcif-examples.
If you plan to use these assembly files for graphical viewing, check if your visualization software (e.g., PyMol, ChimeraX, etc.) supports instantiation of assemblies directly from atomic coordinate files (_struct_assembly related categories), for improved efficiency.
For any further information please email info@wwpdb.org.
[ wwPDB News ]
We are pleased to announce the Protein Data Bank 50th Anniversary Virtual Issue: Featured structural articles from The Journal of Biochemistry were now released in The Journal of Biochemistry (JB).
In this virtual issue, we celebrate the 50th anniversary of the PDB by highlighting the top 10 articles with higher citation numbers and the top 5 articles with the highest resolution published in JB since 1971, together with two papers of 1st NMR structure and one database article in JB.
ModelCIF, an extension of PDBx/mmCIF for computed structure models, is now available. The PDBx/mmCIF data standard underpins the Protein Data Bank (PDB) Core Archive, which is jointly managed by the worldwide Protein Data Bank (wwPDB) consortium. A software library called python-modelcif has been developed to support ModelCIF and enables reading and writing mmCIF files compliant with ModelCIF.
ModelCIF serves as the data standard for representing structural models of macromolecules obtained using computational methods. These computed structure models may be derived from existing structure templates using homology or comparative modeling or can be obtained from ab initio modeling methods. ModelCIF data standard is being adopted by computational biologists as well as major repositories of computed structure models, including ModelArchive, MODBASE, and AlphaFoldDB Protein Structure Database repositories for computed structure models. Partial support for ModelCIF is also available in SWISS-MODEL projects and will soon be added to the SWISS-MODEL Repository.
ModelCIF is developed and maintained by the wwPDB ModelCIF Working Group (WG), consisting of representatives from the wwPDB and the computational structural biology community. The WG is focused on developing common data standards and software tools for archiving and visualization of computed structure models. The WG promotes adoption of ModelCIF within the computational modeling community, and is also involved in developing software tools that support ModelCIF. Research teams making computed structure models available from their own web portals are strongly encouraged to do so using the ModelCIF data standard and integrate them into the 3D-Beacons network. Structural biologists are strongly encouraged to deposit computed structure models to the ModelArchive to ensure long-term preservation and public access. Guidelines on how to deposit computed structure models together with relevant metadata are also available on ELIXIR's RDMkit page for structural bioinformatics.
[ wwPDB News ]
CASP (Critical Assessment of protein Structure Prediction) is in search for targets for the upcoming CASP15 modeling experiment (starting in May 2022). CASP community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. Typically, about 100 modeling groups from around the world participate. Results of CASP experiments are assessed by leaders in the field (Independent Assessors), and published in special issues of the journal PROTEINS.
Following the 2020 CASP14 experiment, it is hard to find a structural biologist who has not heard about the success of deep learning methods in modeling protein structures, particularly by the AlphaFold and more recently RosettaFold. As a result of these advances, computed protein structures are becoming much more widely used in a broadening range of applications. Since CASP14, the protein modeling community has intensified development of these methods and extended their application to include modeling of protein complexes and protein ensembles. CASP15 will provide definitive insight into how successful these new developments are.
CASP15’s success depends on generosity of the experimental community in providing targets as ground truth against which to assess the computation methods. Over the years more than 150 structure determination groups have provided over 1100 targets for CASP challenges. For CASP15, we are requesting submission of all types of experimental structures determined by X-ray crystallography, cryo-electron microscopy and NMR as potential targets, but are particularly interested in the following:
CASP also plans to include modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, and crosslinking mass spectrometry. For that, protein material is needed (this is not expected for most targets, but if available, it would be much appreciated!).
So, if you have suitable targets in any if these areas, we would very much appreciate you getting in touch by replying to this email or writing to casp@predictioncenter.org or suggesting your target directly through the CASP15 target entry page.
Note that CASP target providers are regularly invited to contribute to CASP special journal issue papers (e.g. Computational models in the service of X-ray and cryo-electron microscopy structure determination (2021) Proteins 89: 1633-1646; Target highlights in CASP14: Analysis of models by structure providers (2021) Proteins 89: 1647-1672), and we plan to continue this practice in the future.
[ wwPDB News ]
We are pleased to announce the PDB 50th anniversary article was now released at The Journal of Biochemistry.
As announced previously, deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB) is mandatory as of February 25, 2022. This change is in response to a long-standing community request to the wwPDB EMDB Core Archive and was also a recommendation from the 2020 wwPDB single-particle cryo-EM data-management workshop (white paper in preparation). Several recommendations from this workshop have already been implemented in the wwPDB OneDep system. These include improvements to wwPDB validation reports and enhancements for capturing metadata via the deposition interface.
Mandatory half-maps must be unfiltered, unmasked, unsharpened, and positioned in the same coordinate-space and orientation as the primary map such that they superimpose. The availability of half-maps will contribute to improved validation of EM structures as reflected in the wwPDB validation reports.
wwPDB strongly urges developers of cryo-EM processing software for the affected modalities to implement support for output of such half-maps (if this is not already available).
Any queries about this policy change can be directed to info@wwpdb.org.
[ wwPDB News ]
Starting May 3, 2022, the PDB archive will distribute assembly files in PDBx/mmCIF format, allowing direct access and visualization of the curated assemblies for all PDB entries.
Currently, PDBx/mmCIF formatted assembly files are provided for structures that are non-PDB compliant, however the coordinates use model numbers to differentiate alternate symmetry copies of PDB chain IDs. This method is not ideal, nor necessary, for the current archive PDBx/mmCIF format and has lead to limited use of these files in community software tools. In response to this issue and recommendations by the wwPDB advisory committee, we are implementing updated, standardized practices for generation of assembly files for all PDB entries.
These updated PDBx/mmCIF format assembly files will have improved organization of assembly data to support usage by the community. These files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs (_atom_site.auth_asym_id and _atom_site.label_asym_id) assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules:
In addition, entity ID and chain ID mapping categories will be provided: _pdbx_entity_remapping and _pdbx_chain_remapping.
A new directory (ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/) will be created for the distribution of these updated assembly files. The directory containing the existing assembly mmCIF files for large entries will be removed (ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/).
wwPDB asks all PDB users and software developers to review code and address any limitations related to PDB assemblies. Sample files are made available for testing purposes and to support community adoption at GitHub.com/wwpdb/assembly-mmcif-examples.
If you plan to use these assembly files for graphical viewing, check if your visualization software (e.g., PyMol, ChimeraX, etc.) supports instantiation of assemblies directly from atomic coordinate files (_struct_assembly related categories), you do so for improved efficiency.
For any further information please email info@wwpdb.org.
[ wwPDB News ]
A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 3, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.
The directory 20220103 includes the 185541 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 923 GB.
A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 3, 2022 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20220103/ and ftp://snapshots.pdbj.org/20220103/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (18059 and 254, respectively) and is 4.5 TB in size.
[ wwPDB News ]
226707
PDB entries from 2024-10-30
