News

Update in the number of COVID-19 related structures in the PDB

03 Mar 2021

More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Now Available

With this week's update, 1018 SARS-CoV-2-related structures are now freely available from the Protein Data Bank (PDB).

The first SARS-CoV-2 structure, a high-resolution crystal structure of the coronavirus main protease (PDB 6lu7, shown below), was released early in the pandemic on February 5, 2020.

07 Sep 2020

Congratulations to Olga Kennard on the award of the Ewald Prize

On behalf of EMBL and PDBe, we would like to offer our warmest congratulations to Dr Olga Kennard OBE FRS on the award of the 12th Ewald Prize by the International Union of Crystallography.

See https://www.iucr.org/news/notices/announcements/2020-ewald-prize-winner

PDBe-KB aggregated views for proteins - superimposition and batch downloads

27 Aug 2020

Superimposition and batch downloads added to the PDBe-KB aggregated views

We have introduced some major changes to the PDBe-KB aggregated views of proteins to allow easier in-depth analysis and comparison of protein structures. These changes include comprehensive batch file download options, superimposition and clustering of protein structures, and a raft of other features previously only available through the PDBe-KB COVID-19 portal.

Carbohydrate molecules now have a new representation in the PDB

29 Jul 2020

New branched polysaccharide representation for polymeric carbohydrates in the PDB

The representation of polymeric carbohydrates in the PDB has been updated, including information about linkages between sugars and with standardised nomenclature, while the PDBe website now includes improved visualisation of these molecules and their interactions.

 

Improved Carbohydrate Data at the PDB

08 Jul 2020

Coming July 29: Improved Carbohydrate Data at the PDB

PDB data will incorporate a new data representation for carbohydrates in PDB entries and reference data that improves the Findability and Interoperability of these molecules in macromolecular structures.

In order to remediate and improve the representation of carbohydrates across the archive, the wwPDB has:

PDBe-KB COVID-19 data portal - aggregated views for proteins

16 Jun 2020

COVID-19 data on PDBe-KB pages now focused around specific proteins

We have now added dedicated pages to the PDBe-KB COVID-19 data portal that display all structural data for specific, mature proteins, therefore making it easier for users to find the exact information they need to support the development of vaccines and therapeutics to compact this pandemic.

 

PDBe-KB COVID-19 pages

06 May 2020

More download options and antibody annotations on the PDBe-KB COVID-19 pages

We recently announced the new PDBe-KB COVID-19 data portal (pdbe.org/covid19), allowing users to easily access a wealth of structural data from the SARS-CoV-2 virus. We have now added annotations on antibody classifications and details of peptide inhibitor molecules to the interactions section. In addition, we have also extended the bulk download options to entries with specific ligands or macromolecular interactions.

New ProtVista and LigEnv components at PDBe

23 Apr 2020

Test the new sequence and ligand components at PDBe

 

We are delighted to offer two new components available for beta testing on our PDBe entry pages: the ProtVista sequence component on the PDBe macromolecules pages and the LigEnv component on the ligands and environments pages.

Try the ProtVista component on our macromolecules page here.

PDBe-KB COVID-19 Data Portal - more features added

17 Apr 2020

Download service and similar proteins data added to PDBe-KB COVID-19 pages

We recently announced the new PDBe-KB COVID-19 data portal, allowing users to easily access a wealth of structural data from the SARS-CoV-2 virus. We have now added more functionality to these pages, allowing bulk download of all relevant PDB structures and highlighting all the PDB entries with high sequence identity to SARS-CoV-2 proteins.

PDBe-KB COVID-19 data portal

03 Apr 2020

New PDBe-KB COVID-19 Data Portal

Our new PDBe-KB COVID-19 data portal brings together all available PDB data from SARS-CoV-2 structures, to help researchers easily identify important structural features to support the development of treatments and vaccines.

Visit the PDBe-KB COVID-19 data portal

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