PDBe-KB: a community-driven resource for structural and functional annotations

Article Article scientifique Article PDBe-KB: a community-driven resource for structural and functional annotations eng 2019-10-04 2020-01-08 PDBe-KB consortium author Varadi Mihaly European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 666399 author Berrisford John European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Deshpande Mandar European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Nair Sreenath S. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Gutmanas Aleksandras European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Armstrong David European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Pravda Lukas European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Al-Lazikani Bissan Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK author Anyango Stephen European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Barton Geoffrey J. School of Life Sciences, University of Dundee, Dundee, UK author Berka Karel Department of Physical Chemistry, Palacky University, Olomouc author Blundell Tom University of Cambridge, Cambridge, UK author Borkakoti Neera European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Dana Jose European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Das Sayoni Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK author Dey Sucharita Weizmann Institute of Science, Rehovot, Israel author Micco Patrizio Di Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK author Fraternali Franca Randall Centre for Cell & Molecular Biophysics, King's College London, London, UK author Gibson Toby European Molecular Biology Laboratory, Heidelberg, Germany author Helmer-Citterich Manuela Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy author Hoksza David Charles University, Prague, Czech Republic author Huang Liang-Chin Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA author Jain Rishabh European Molecular Biology Laboratory, Heidelberg, Germany author Jubb Harry Cresset, Cambridgeshire, UK author Kannas Christos Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK author Kannan Natarajan Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA author Koca Jaroslav CEITEC, Central European Institute of Technology, Masaryk University, Brno, Czech Republic author Krivak Radoslav Charles University, Prague, Czech Republic author Kumar Manjeet European Molecular Biology Laboratory, Heidelberg, Germany author Levy Emmanuel Weizmann Institute of Science, Rehovot, Israel 417450 Département de biologie moléculaire et cellulaire (MOCEL) author Madeira F. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Madhusudhan M. S. Indian Institute of Science Education and Research, Pune 411008, India author Martell Henry J. University of Kent, Canterbury, Kent, CT2 7NJ, UK author MacGowan Stuart School of Life Sciences, University of Dundee, Dundee, UK author McGreig Jake E. University of Kent, Canterbury, Kent, CT2 7NJ, UK author Mir Saqib European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Mukhopadhyay Abhik European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Parca Luca Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy author Paysan-Lafosse Typhaine European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Radusky Leandro Centre for Genomic Regulation (CRG), Barcelona, Spain author Sousa Ribeiro Jose Antonio European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 807822 author Serrano Nikolaus Luis Enrique Centre for Genomic Regulation (CRG), Barcelona, Spain 417278 author Sillitoe Ian Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK author Singh Gulzar Indian Institute of Science Education and Research, Pune 411008, India author Skoda Petr Charles University, Prague, Czech Republic author Svobodova Radka CEITEC, Central European Institute of Technology, Masaryk University, Brno, Czech Republic author Tyzack Jonathan European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Valencia Alfonso Barcelona Supercomputing Center, Barcelona, Spain 31280 author Fernandez Eloy Villasclaras Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK author Vranken Wim Vrije Universiteit Brussel, Brussels, Belgium author Wass Mark University of Kent, Canterbury, Kent, CT2 7NJ, UK author Thornton Janet European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK author Sternberg Michael Imperial College London, London, UK author Orengo Christine Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK author Velankar Sameer European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK D344-D353 10.1093/nar/gkz853 31584092 0305-1048 PMC6943075 https://academic.oup.com/nar/article/48/D1/D344/5580911 <p>The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages—the PDBe-KB aggregated views of structure data—which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.</p> National Institutes of Health A data analytics framework for mining the dark kinome 1U01CA239106-01 US NATIONAL CANCER INSTITUTE UK Research and Innovation India partnering award: Sustainable data archiving and dissemination strategy to support data driven biology BB/P025846/1 GB BBSRC UK Research and Innovation Expanding Genome3D and disseminating the structural annotations via InterPro and PDBe BB/N019172/1 GB BBSRC UK Research and Innovation The Dundee Resource for Protein Structure Prediction and Sequence Analysis BB/J019364/1 GB BBSRC UK Research and Innovation Expanding the knowledge of structures and functional information through the SIFTS resource BB/M011674/1 GB BBSRC UK Research and Innovation FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration BB/P024351/1 GB BBSRC Hermesfonds for ELIXIR Belgium AH.2017.051 Biotechnology and Biological Sciences Research Council BB/H018409/1 European Regional Development Fund CZ.02.1.01/0.0/0.0/16_013/0001777 NIH R01GM1149 Wellcome Trust Strategic Awards WT09230 Wellcome Trust 100150/Z/12/Z Medical Research Council MR/L01257X/1 Czech Science Foundation 17-21122S AIRC IG 16895 ELIXIR CZ Research Infrastructure Project LM2015047 NIGMS NIH HHS R01 GM114409 NCI NIH HHS U01 CA239106 Cancer Research UK 23187 Engineering and Physical Sciences Research Council 1953183 Research Foundation Flanders G.0328.16N British Heart Foundation NH/12/2/29427 true Nucleic acids research 48 D1 56d05df0-fad0-4484-a138-0e131c49014b Article (Published version) Public Article-scientifique-from-unpaywall.pdf 3005567 application/pdf CC BY-4.0 7aaa0455dcb641481cd109e324e5badb05afe42d27f98d8d15b367e01ffcfb59 openAccess

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PDBe-KB: a community-driven resource for structural and functional annotations	Nucleic acids research			2020	69	31

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Sousa Ribeiro, Jose Antonio