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

PDBe-KB COVID-19 Data Portal - more features added
17 April 2020

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.

To support SARS-CoV-2 research efforts, we aim to provide as much relevant structure data as possible through the PDBe-KB COVID-19 data portal. This means that we are actively working on adding new functionality to these pages, which in the future will also be incorporated into our standard PDBe-KB pages.

One major development on these pages is the addition of a bulk download option, allowing users to easily download all the PDB structures mapped to that Uniprot accession for further analysis. Furthermore, there are also bulk download options for ligands and interactions, allowing you to download all PDB entries with a specific small molecule bound or a specific binding partner. For example, for the PDBe-KB COVID-19 spike glycoprotein there are 10 structures in the PDB - clicking the download button below the ‘structures’ summary icon allows you to download all of these PDB structures.

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We have also extended our ‘similar proteins’ section for the PDBe-KB COVID-19 pages, to include all the data available from closely related organisms, expanding the amount of relevant information that is easily accessible. This section now includes all PDB entries that have at least 90% sequence identity to the SARS-CoV-2 protein, bringing together all near-identical proteins from closely related organisms. On the Replicase polyprotein 1ab COVID-19 page, there are 9 additional similar proteins from different strains of SARS, making data for over 150 additional protein structures easily accessible. 

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The PDBe team is continuing to work hard on creating additional functionality for these COVID-19 pages. Please keep an eye out for further information about these new features in the coming weeks.

If you have any feedback or queries about these pages, then please do not hesitate to get in touch at pdbehelp@ebi.ac.uk.