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Nadpis Prezentace Re-use of data in the field of structural biology Radka Svobodová Vařeková CEITEC, Masaryk University 21st Century – “Century of life science data” ? Nucleic acid sequences Drug-like molecules European Nucleotide Archive PubChem ArrayExpress Zinc Expression Atlas DrugBank … Protein PDB CCD (biomacromolecule) ChEBI structures ChEMBL … Protein Data Bank 2 21st Century – “Century of life science data” ? Nucleic acid sequences Drug-like molecules Structural biology European Nucleotide Archive PubChem ArrayExpress Zinc Expression Atlas DrugBank … Protein PDB CCD (biomacromolecule) ChEBI structures ChEMBL … Protein Data Bank 3 Structural biology 3D structures of biomacromolecules 89% X-ray 10% NMR 1% cryo-electron crystallografy spectroscopy microscopy 3D structure ... ATOM 46 C GLY A 70 51.536 23.360 40.507 ATOM 47 O GLY A 70 50.947 22.279 40.325 ATOM 48 N ILE A 71 50.965 24.532 40.270 ATOM 49 CA ILE A 71 49.595 24.644 39.786 ... 4 Protein Data Bank > 130k biomacromolecular structures Sustainability and re-usability granted :-))) 5 Results based on this data A lot of articles were published … … and 14 Nobel prizes awarded: Chemistry 2013: Martin Karplus (1/3), Michael Levitt (1/3) and Arieh Warshel (1/3). Development of multiscale models for complex chemical systems Chemistry 2009: Venkatraman Ramakrishnan (1/3), Thomas A. Steitz (1/3) and Ada E. Yonath (1/3). Studies of the structure and function of the ribosome. Chemistry 2006: Roger D. Kornberg (1). Studies of the molecular basis of eukaryotic transcription. plus 11 more, see here: http://www.ebi.ac.uk/pdbe/docs/nobel/nobels.html 6 Secondary data • Obtained during analysis and processing of primary PDB data • Examples: • Validation reports • Biomacromolecular channels • Catalytic active sites • Protein families • Secondary structure elements • Simulation results: • Homology models • Molecular dynamics • Docking outputs • Predicted prperties • Often huge amounts of data • Sustainability and re-usability is a challenge 7 How to make the life science data sustainable and re-usable? Nucleic acid Biomacromolecular Drug-like molecules sequences structures European Nucleotide Archive PubChem, Zinc, Protein Data Bank ArrayExpress DrugBank, PDB CCD, Expression Atla ChEBI, ChEMBL … + all the secondary data 8 ELIXIR • A distributed infrastructure for life-science information • European Bioinformatics Institute (EMBL-EBI) in UK as a hub • 20 countries (ELIXIR nodes) • Czech Republic is ELIXIR node from 2013 7 ELIXIR CZ 14 members: • Institute of Organic Chemistry and Biochemistry of the CAS (Hub) • Masaryk University – CEITEC and CERIT–SC • CESNET • Palacký University Olomouc • Charles University • Institute of Molecular Genetics of the ASCR, v. v. i. • Institute of Microbiology of the CAS, v. v. i. • Institute of Biotechnology CAS, v. v. i. • Biology Centre CAS • University of Chemistry and Technology, Prague • Czech Technical University in Prague - Faculty of Information Technology • University of West Bohemia • University of South Bohemia in České Budějovice • University Hospital at Saint Anna in Brno, FNUSA – ICRC Belongs to a roadmap of Czech Research infrastructures Funded by national and international grants 10 ELIXIR Platforms 11 ELIXIR Platforms 12 ELIXIR Data FAIR Data Findable Citable Accessible Trackable & Countable Interoperable Intelligible Reusable Reproducible 13 Thank you for your attention Central European Institute of Technology Masaryk University Kamenice 753/5 625 00 Brno, Czech Republic www.ceitec.muni.czWe are | [email protected] looking forward to cooperation with you ..
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