Dear CCP4BB
We have introduced some major changes to the <https://www.ebi.ac.uk/pdbe/pdbe-kb/protein> 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 <https://www.ebi.ac.uk/pdbe/covid-19> PDBe-KB COVID-19 portal. We have introduced a process that superimposes structures for a given protein in the PDB based on their structural similarity. This enables users of our PDBe-KB protein aggregated views to easily identify unique structural conformations for each discrete section ("segment") of sequence for a given UniProt entry. It also allows easy visualisation of all ligands that interact with this segment of the protein. These structural clusters can be easily displayed in your browser using the <https://www.ebi.ac.uk/pdbe/about/news/introducing-mol-fast-interactive-3d-v isualisation-your-browser-rcsb-pdb-and-pdbe> Mol* visualisation software. Also introduced in this update to the PDBe-KB aggregated views is a new batch download service, allowing users to download all files for a specific subset of entries. We have also integrated a number of features into the all PDBe-KB aggregated views that were previously only available in the PDBe-KB COVID-19 portal, including better handling of viral polyproteins, expanding of the similar proteins section to the whole PDB, and highlighting of interactions for molecules annotated as antibodies and PRDs (Peptide Reference Dictionary). To try these new features, visit any PDBe-KB aggregated views page - for example, you can view the page for the COVID-19 main protease at <https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/PRO_0000449623> https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/PRO_0000449623. For more information about these changes, please visit <https://www.ebi.ac.uk/pdbe/about/news/superimposition-and-batch-downloads-a dded-pdbe-kb-aggregated-views> https://www.ebi.ac.uk/pdbe/about/news/superimposition-and-batch-downloads-ad ded-pdbe-kb-aggregated-views Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
