News

wwPDB news banner image with virus structure in background

wwPDB News: PDB entries with new ligands only in PDBx/mmCIF format

At current growth rates, we anticipate running out of three-character Chemical Component IDs by the end of 2023. After this point, the wwPDB will issue five-character alphanumeric accession codes for CCD IDs in the OneDep system.

Image displaying event information for the 2023 PDB Art exhibition opening with a colourful artwork displayed in the background.

PDB Art Virtual Exhibition 2023 - Opening Event

Protein Data Bank in Europe (PDBe) are hosting an online art exhibition to celebrate artwork created through the PDB Art project in 2023. This virtual event, on Tuesday 19th September 2023 at 5:00pm BST, will mark the official opening of the 2023 virtual exhibition.

Title image introducing covalently linked components with complex, multi-component ligand image displayed in the background.

Introducing ‘Covalently Linked Components’ and enriched ligand information at PDBe

We have introduced Covalently Linked Components (CLCs), a new class of reference small molecules simplifying the identification of multi-component ligands in PDB entries, plus we have enhanced the content of wwPDB CCD and PRD files with valuable meta-data.

Title image with structure in background, announcing the new PDBImages pipeline

PDBImages: A new, open-source macromolecular structure imaging pipeline

The PDBe team, in collaboration with David Sehnal (NCBR, Masaryk University, Czech Republic), has developed a new pipeline for generating images of macromolecular structures.

3D-Beacons logo and resource name to highlight release of the new version. A protein structure is shown in the background of the image.

3D-Beacons update: Search for structural models by protein sequence

The 3D-Beacons resource has undergone some major improvements, including updates to the API and a new sequence search feature.

wwPDB news banner image

wwPDB news: Updated Annotation and Standardization of Peptide Residues

In October 2023, wwPDB will roll out updated CCD data files with additional annotation and standardized atom naming of peptide residues.

Image to promote the superposition tool at PDBe-KB, enabling better identification of structure conformations in the PDB archive

Illuminating protein conformational landscapes in the PDB archive

The PDBe team is excited to announce the release of a groundbreaking scientific data pipeline to identify protein conformational states in the Protein Data Bank (PDB).

Worldwide Protein Data Bank (wwPDB) 20 years logo

wwPDB News - 20 Years of the wwPDB and PDBc associate member

Celebrating 20 years of the wwPDB consortium and announcing the launch of Protein Data Bank China (PDBc) as an Associate Member of the Partnership.

wwPDB news banner image

wwPDB News - NMR restraint remediation conforms to standard NMR-STAR and NEF format

Standardized NMR data files and updated validation reports are now available for existing NMR entries

wwPDB news banner image

wwPDB news: NMR restraint remediation conforms to standard NMR-STAR and NEF format

NMR data files are standardized in NEF and NMR-STAR format [Ulrich, 2019] for the PDB entries which have NMR data in many different software specific formats.

Interactions displayed between proteins in a structure, which are analysed by the PISAlite software

Improved macromolecular interactions data with PISA-lite

An updated version of PISA generates new and enhanced interactions data for all annotated assemblies in the PDB archive, available from the PDBe API and FTP.

Image of hemoglobin complex highlighting the complex ID and components of the complex

A new process for aggregating and naming assemblies in the PDB

PDBe has created a new process to aggregate and name assemblies in the PDB based on unique assembly composition.