“EXPERT” A Practical and Forward-Looking Guide to Capturing Protein Expression and Purification Metadata to develop Machine Learning Models
Journal of Biological Chemistry, pp. 113610
Abstract
As machine learning (ML) becomes increasingly important in protein engineering, synthetic biology, and bioprocess optimisation, the lack of consistent, complete, and standardised experimental reporting remains a major barrier to building effective models. EXPERT (EXpression and Purification Experimental Reporting Template) defines a structured framework for capturing protein expression and purification data across the community, to increase reproducibility across laboratories and support downstream ML applications. We propose here the essential data that should be recorded during expression and purification workflows by both novice and experienced protein production scientists. Its recommendations are informed by expert contributions from across academia and industry. The reporting requirements were distilled to a focused set of parameters deemed sufficient for workflow reproducibility and constructing robust ML models aimed at improving protein production. By deploying these guidelines, we hope to enable the collection of larger data sets to support future model building.
Authors 86
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Affiliation as printed
School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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European Bioinformatics Institute
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European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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Protein Express (United States) · European Molecular Biology Laboratory
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European Molecular Biology Laboratory, Protein Expression and Purification Core Facility, Heidelberg, Germany
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Centre National de la Recherche Scientifique · Université Paris Sciences et Lettres
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Institut curie, curiecoretech, PSL University, Recombinant Proteins core facility, CNRS Paris, France
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Structural Genomics Consortium
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Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, ON, Canada
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European Bioinformatics Institute
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European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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Membrane Protein Laboratory, Research Complex at Harwell, Diamond Light Source, Harwell Oxford, Didcot, UK
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Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform for Protein Production & Characterization, Berlin, Germany
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Fraunhofer Institute for Cell Therapy and Immunology
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Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
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Laboratory of Environmental and Life Science, University of Nova Gorica, Rožna Dolina (Nova Gorica), Slovenia
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Science for Life Laboratory · KTH Royal Institute of Technology
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Department of Protein Science, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
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Max Planck Institute of Molecular Cell Biology and Genetics
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Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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biomodal, Chesterford Research Park, Cambridge, UK
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Technical University of Denmark
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Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Barcelona Institute of Science and Technology · Centre for Genomic Regulation
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Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
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Affiliation as printed
Kemp Proteins, LLC, Frederick, MD 21704, USA
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Protein Express (United States)
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Mammalian Protein Expression core facility and Protein Production Sweden, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Pfizer Research and Development, Cambridge, USA
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Vienna BioCenter Core Facilities
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Vienna BioCenter Core Facilities GmbH, Vienna, Austria
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Institute of Structural and Molecular Biology · University College London
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University College London, Dept of Computer Science and Department of Structural and Molecular Biology, Gower Street, London, UK
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Generative Biology Institute, Ellison Institute of Technology Oxford, The Oxford Science Park, Oxford, UK; School of Informatics, The University of Edinburgh, UK; School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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Septerna, South San Francisco, USA
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Max Planck Institute of Molecular Cell Biology and Genetics
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Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Lund Protein Production Platform & Protein Production Sweden & Science for Life Laboratory, Lund University, Lund, Sweden
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Institute of Biophysical Chemistry, Goethe-University Frankfurt, Frankfurt/Main, Germany
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i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto
Affiliation as printed
i3s - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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Science for Life Laboratory · KTH Royal Institute of Technology
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Department of Protein Science, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
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Novartis, Biomedical Research, Cambridge, MA, USA
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Max Planck-Bristol Centre for Minimal Biology
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Max Planck-Bristol Centre for Minimal Biology, Schools of Chemistry and Biochemistry, University of Bristol, Bristol, UK
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Protein Express (United States)
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Executive Editor, Protein Expression and Purification Journal, London, UK
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Czech Academy of Sciences, Institute of Biotechnology
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Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
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UCL School of Pharmacy · University College London
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School of Pharmacy and Structural Genomics Consortium, UCL, London, UK
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Max Planck Institute of Biochemistry
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Max Planck Institute of Biochemistry, Protein Production and Structural Validation Facility, 82152 Martinsried, Germany
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Cleveland Clinic Center for Therapeutics Discovery, Cleveland Clinic Research, Cleveland, USA
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BOKU University, Department of Biotechnology and Food Science (BTLW), Institute of Bioprocess Science and Engineering (IBSE), 1190 Vienna, Austria
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Helmholtz Centre for Infection Research
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Helmholtz Centre for Infection Research, Department of Molecular Structural Biology (MOSB), Braunschweig, Germany
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VIB-UGent Center for Plant Systems Biology · VIB-UGent Center for Inflammation Research
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VIB Protein Core, VIB Technologies, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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Kavli Institute of Nanoscience Discovery, University of Oxford, Department of Chemistry, Oxford, UK
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École Polytechnique Fédérale de Lausanne
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Protein Production and Structure Characterization Core Facility (PTPSP), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Department of Chemistry and Molecular Biology, Biochemistry, University of Gothenburg, Göteborg, Sweden
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Structural Genomics Consortium
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Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, ON, Canada
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Structural Genomics Consortium
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Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, ON, Canada
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Abcam (United States) · Abcam (United Kingdom)
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Abcam, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK
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European Institute of Oncology
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Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Milan, Italy
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Protein Express (United States)
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Mammalian Protein Expression core facility and Protein Production Sweden, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Helmholtz Centre for Infection Research
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Virus-like-particle based technologies, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Sygnature Discovery, Pennyfoot Street, Nottingham, UK
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European Molecular Biology Laboratory
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European Molecular Biology Laboratory, Grenoble, Cedex, France
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UCL School of Pharmacy · University College London
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School of Pharmacy and Structural Genomics Consortium, UCL, London, UK
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Structural Genomics Consortium
Affiliation as printed
Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, ON, Canada
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Czech Academy of Sciences, Institute of Biotechnology
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Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
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Institute for Research in Biomedicine
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Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Data
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Powered Therapeutics GmbH, Annastraße 27, 37075 Göttingen, Germany
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Medicine Design, Pfizer Worldwide R&D, San Diego CA USA
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Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
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Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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Concept Life Sciences (United Kingdom)
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Concept Life Sciences, Edinburgh, UK
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Elettra-Sincrotrone Trieste S.C.p.A.
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Protein Targets for Drug Discovery Lab, Structural Biology, Elettra Sincrotrone Trieste, S.S. AREA Science Park, Basovizza, Trieste, ITALY
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NKI Protein facility, Division of Biochemistry, The Netherlands Cancer Institute (NKI), CX Amsterdam, The Netherlands
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Viva Shanghai 201318, China
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Structural Genomics Consortium
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Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, ON, Canada
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Structural Genomics Consortium
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Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, ON, Canada
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The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK and Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Centre National de la Recherche Scientifique
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AFMB UMR 7257 CNRS-AMU, MARSEILLE Cedex 09, France
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Thomson Reuters (United States)
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Thomson Instrument Company, Carlsbad, CA, USA
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Sygnature Discovery, Pennyfoot Street, Nottingham, UK
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Institute for Protein Innovation
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Institute for Protein Innovation, Boston, MA, USA
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Leiden University Medical Center
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Dept. of Cell and Chemical Biology (CCB), Leiden University Medical Centre (LUMC), Leiden, The Netherlands
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Protein Express (United States)
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The Jackson Laboratory, Protein Science Services, ME, USA
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Fraunhofer Institute for Translational Medicine and Pharmacology
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Fraunhofer Institute for Translational Medicine and Pharmacology ITMP; Immunology, Infection and Pandemic Research IIP, Penzberg, Germany
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European Bioinformatics Institute
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European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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Human Technopole, Viale Rita, Milan, Italy
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Data Sciences and Quantitative Biology, Discovery Sciences, R&D BioPharmaceuticals, Cambridge, UK
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Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité
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Institut Pasteur, Université Paris Cité, Production and Purification of recombinant Proteins core facility, CNRS UMR3528, Paris, France
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Sygnature Discovery, Pennyfoot Street, Nottingham, UK
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Universität Hamburg · University Medical Center Hamburg-Eppendorf
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Protein Production Core Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
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Structural Biology STP, Francis Crick Institute, London
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Life Sciences Core Facilities (LSCF), Structural Proteomics Unit (SPU), Weizmann Institute of Science, Rehovot, Israel
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Medicine Design, Pfizer Worldwide R&D, Groton CT, USA
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Hebrew University of Jerusalem
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Protein Expression Facility, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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European Bioinformatics Institute
Affiliation as printed
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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Affiliation as printed
Lund Protein Production Platform & Protein Production Sweden & Science for Life Laboratory, Lund University, Lund, Sweden
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Fraunhofer Institute for Translational Medicine and Pharmacology
Affiliation as printed
Fraunhofer Institute for Translational Medicine and Pharmacology ITMP; Immunology, Infection and Pandemic Research IIP, Penzberg, Germany
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Affiliation as printed
Life Sciences Core Facilities (LSCF), Structural Proteomics Unit (SPU), Weizmann Institute of Science, Rehovot, Israel
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Lovisa Holmberg Schiavone corresponding
Affiliation as printed
Protein Sciences, Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden. Electronic address: Lovisa.Holmberg.Schiavone@astrazeneca.com
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N. Burgess-Brown corresponding
UCL School of Pharmacy · University College London
Affiliation as printed
School of Pharmacy and Structural Genomics Consortium, UCL, London, UK. Electronic address: n.burgess-brown@ucl.ac.uk
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