wwPDB 2023 News

Contents

02/06/2023 Prototype of PDB NextGen Archive now available
01/31/2023 Enhanced Collection of Starting Models
01/30/2023 Structure Predictors: Use ModelCIF for Computed Structure Models
01/10/2023 PDB Reaches a New Milestone: 200,000+ Entries
01/03/2023 Time-stamped Copies of PDB and EMDB Archives

02/06/2023

Prototype of PDB NextGen Archive now available

A prototype of a next generation archive repository for the PDB is now available. The archive, called “NextGen”, hosts structural model files in PDBx/mmCIF and PDBML formats at files-nextgen.wwpdb.org. This enriched PDB archive provides annotation from external database resources in the metadata in addition to the content provided in the structure model files in the PDB main archive at files.wwpdb.org.

This prototype provides sequence annotation from external resources such as UniProt, SCOP2 and Pfam at atom, residue, and chain levels. This mapping information is derived from the Structure Integration with Function, Taxonomy and Sequence (SIFTS) project (https://www.ebi.ac.uk/pdbe/docs/sifts/), a service developed and maintained by the PDBe and UniProt teams at EMBL-EBI. Sequence mappings are provided in _pdbx_sifts_unp_segments and _pdbx_sifts_xref_db_segments categories for each segment, _pdbx_sifts_xref_db at residue level, and _atom_site at atom level.

The PDB NextGen Repository is currently updated monthly on the first Wednesday of the month at 00:00 UTC and is subject to change in the future. You can access these NextGen files at the following locations:

Data are structured based on entry ID with a two letter hash code, ‘third from last character' and 'second from last character’. This hash code will remain consistent once PDB ID codes are extended beyond four characters with the pdb_ prefix.

Some examples are shown below:

  • Access entry pdb_00008aly at https://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_00008aly/
  • Both PDBx/mmCIF and PDBML are provided at this location. For entry pdb_00008aly:
    • pdb_00008aly_xyz-enrich.cif.gz
    • 
pdb_00008aly_xyz-no-atom-enrich.xml.gz

    Please contact info@wwpdb.org with any questions.

    01/31/2023

    Enhanced Collection of Starting Models

    A new PDBx/mmCIF category, _pdbx_initial_refinement_model has been introduced to improve information collected about starting model for X-ray, 3DEM and NMR methods.

    Experimentally derived vs computed models will be distinguished. Provenances of the resources where the starting model was obtained (e.g., PDB, AlphaFoldDB, RoseTTAFold, etc.) and its accession code/identifier will be captured, if publicly available.

    For the full definition, see pdbx_initial_refinement_model. An example is below:

    _pdbx_initial_refinement_model.id 1
    _pdbx_initial_refinement_model.entity_id_list 1
    _pdbx_initial_refinement_model.type 'experimental model'
    _pdbx_initial_refinement_model.source_name PDB
    _pdbx_initial_refinement_model.accession_code 3LTQ

    wwPDB strongly recommends all PDB users and software developers to review their code and adopt this definition for future applications.

    01/30/2023

    Structure Predictors: Use ModelCIF for Computed Structure Models

    ModelCIF (GitHub) is a data information framework developed for and by computational structural biologists to describe structural models of macromolecules derived from computational methods. It provides an extensible data representation for deposition, archiving, and public dissemination of these models of proteins to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide.

    <I>A. Overview of the ModelCIF extension of PDBx/mmCIF. B. Schematic representation of ModelCIF data specifications. ModelCIF includes definitions for input data used in template-based and template-free modeling; reference information for macromolecular sequences and small molecule components; local and global CSM quality metrics; and metadata information regarding modeling protocol, CSM classification (ab initio, homology, etc.) and descriptions of associated files.</I>A. Overview of the ModelCIF extension of PDBx/mmCIF. B. Schematic representation of ModelCIF data specifications. ModelCIF includes definitions for input data used in template-based and template-free modeling; reference information for macromolecular sequences and small molecule components; local and global CSM quality metrics; and metadata information regarding modeling protocol, CSM classification (ab initio, homology, etc.) and descriptions of associated files.

    ModelCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined, three-dimensional (3D) structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the wwPDB in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group.

    This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Furthermore, use of this data standard promotes interoperation among structural biology data resources, with ModelCIF currently used by the ModelArchive, AlphaFold DB, and MODBASE repositories. A manuscript was recently submitted to bioRxiv describing the architecture, contents, and governance of ModelCIF as well as tools and processes for maintaining and extending the data standard [1].

    Visit the ModelCIF GitHub for more information about this data information framework.

    [1} Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, et al. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. bioRxiv doi: 10.1101/2022.12.06.518550.

    01/10/2023

    PDB Reaches a New Milestone: 200,000+ Entries

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    With this week's update, the PDB archive contains a record 200,069 entries. The archive passed 150,000 structures in 2019 and 100,000 structures in 2014.

    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.

    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. Many milestones have been reached since the archive released the 100,000th structure in 2014. PDB data have been seminal in understanding SARS-CoV-2, and provided the foundation for the development of AI/ML techniques for predicting protein structure. The 50th anniversary of the PDB was celebrated throughout 2021.

    Today, the archive is quite large, containing more than 3,000,000 files related to these PDB entries that require more than 1086 Gbytes of storage. PDB structures contain more than 1.8 billion non-hydrogen atoms.

    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 266 new structures into the archive. These structures join others vital to drug discovery, bioinformatics and education.

    The PDB is growing rapidly, increasing in size by ~160% since 2011 (doubling in size every 6-8 years). In 2022, an average of 275 new structures were released to the scientific community each 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.

    Twenty Years of Collaboration

    Since its inception, the PDB has been a community-driven enterprise, evolving into a mission critical international resource for biological research. The wwPDB partnership was established in July 2003 with PDBe, PDBj, and RCSB PDB. Today, the collaboration includes partners BMRB (joined in 2006) and EMDB (2021).

    The wwPDB ensures that these valuable PDB 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.

    wwPDB eagerly awaits the next 100,000 structures and the invaluable knowledge these new data will bring.

    01/03/2023

    Time-stamped Copies of PDB and EMDB Archives

    <I>A snapshot of the PDB Core Archive as of January 2, 2023 is available. </I>A snapshot of the PDB Core Archive as of January 2, 2023 is available.

    A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org, https://s3.rcsb.org) as of January 2, 2023 has been added to ftp://snapshots.wwpdb.org, https://s3snapshots.rcsb.org (AWS), 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 20230102 includes the 199,755 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 1086 GB.

    A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 2, 2023 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20230102/ and ftp://snapshots.pdbj.org/20230102/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (24186 and 262, respectively) and is 8.9 TB in size.