1. Structural Biology and Molecular Biophysics
  2. Computational and Systems Biology
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Building bridges between cellular and molecular structural biology

  1. Ardan Patwardhan  Is a corresponding author
  2. Robert Brandt
  3. Sarah J Butcher
  4. Lucy Collinson
  5. David Gault
  6. Kay Grünewald
  7. Corey Hecksel
  8. Juha T Huiskonen
  9. Andrii Iudin
  10. Martin L Jones
  11. Paul K Korir
  12. Abraham J Koster
  13. Ingvar Lagerstedt
  14. Catherine L Lawson
  15. David Mastronarde
  16. Matthew McCormick
  17. Helen Parkinson
  18. Peter B Rosenthal
  19. Stephan Saalfeld
  20. Helen R Saibil
  21. Sirarat Sarntivijai
  22. Irene Solanes Valero
  23. Sriram Subramaniam
  24. Jason R Swedlow
  25. Ilinca Tudose
  26. Martyn Winn
  27. Gerard J Kleywegt  Is a corresponding author
  1. European Bioinformatics Institute, United Kingdom
  2. FEI Company, France
  3. University of Helsinki, Finland
  4. Francis Crick Institute, United Kingdom
  5. University of Dundee, United Kingdom
  6. University of Oxford, United Kingdom
  7. Diamond Light Source Ltd, United Kingdom
  8. European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
  9. London Research Institute, United Kingdom
  10. Leiden University Medical Center, Netherlands
  11. Lilly UK, United Kingdom
  12. The State University of New Jersey, United States
  13. University of Colorado, United States
  14. Kitware, Inc., United States
  15. The Francis Crick Institute, United Kingdom
  16. Janelia Research Campus, Howard Hughes Medical Institute, United States
  17. Birkbeck College, United Kingdom
  18. University of Vic - Central University of Catalonia, Spain
  19. National Cancer Institute, United States
  20. Science and Technology Facilities Council, United Kingdom
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Cite this article as: eLife 2017;6:e25835 doi: 10.7554/eLife.25835

Abstract

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Article and author information

Author details

  1. Ardan Patwardhan

    Cellular Structure and 3D Bioimaging, European Bioinformatics Institute, Hinxton, United Kingdom
    For correspondence
    ardan@ebi.ac.uk
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7663-9028
  2. Robert Brandt

    Visualization Sciences Group, FEI Company, Mérignac, France
    Competing interests
    No competing interests declared.
  3. Sarah J Butcher

    Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  4. Lucy Collinson

    Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
    Competing interests
    No competing interests declared.
  5. David Gault

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    No competing interests declared.
  6. Kay Grünewald

    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  7. Corey Hecksel

    Electron Bio-Imaging Centre, Diamond Light Source Ltd, Didcot, United Kingdom
    Competing interests
    No competing interests declared.
  8. Juha T Huiskonen

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  9. Andrii Iudin

    Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
    Competing interests
    No competing interests declared.
  10. Martin L Jones

    Vascular Biology Laboratory, London Research Institute, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0994-5652
  11. Paul K Korir

    Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
    Competing interests
    No competing interests declared.
  12. Abraham J Koster

    Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, Netherlands
    Competing interests
    No competing interests declared.
  13. Ingvar Lagerstedt

    Computational Chemistry and Cheminformatics, Lilly UK, Windlesham, United Kingdom
    Competing interests
    No competing interests declared.
  14. Catherine L Lawson

    Center for Integrative Proteomics Research and Research Collaboratory for Structural Bioinformatics, The State University of New Jersey, New Jersey, United States
    Competing interests
    No competing interests declared.
  15. David Mastronarde

    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Colorado, United States
    Competing interests
    No competing interests declared.
  16. Matthew McCormick

    Kitware, Inc., Carrboro, United States
    Competing interests
    No competing interests declared.
  17. Helen Parkinson

    Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
    Competing interests
    No competing interests declared.
  18. Peter B Rosenthal

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    No competing interests declared.
  19. Stephan Saalfeld

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4106-1761
  20. Helen R Saibil

    Department of Crystallography, Birkbeck College, London, United Kingdom
    Competing interests
    No competing interests declared.
  21. Sirarat Sarntivijai

    Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
    Competing interests
    No competing interests declared.
  22. Irene Solanes Valero

    Degree in Biotechnology, University of Vic - Central University of Catalonia, Barcelona, Spain
    Competing interests
    No competing interests declared.
  23. Sriram Subramaniam

    Laboratory of Cell Biology, CCR, National Cancer Institute, Bethesda, United States
    Competing interests
    Sriram Subramaniam, Reviewing editor, eLife.
  24. Jason R Swedlow

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    No competing interests declared.
  25. Ilinca Tudose

    Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
    Competing interests
    No competing interests declared.
  26. Martyn Winn

    Scientific Computing Department, Science and Technology Facilities Council, Didcot, United Kingdom
    Competing interests
    No competing interests declared.
  27. Gerard J Kleywegt

    Molecular and Cellular Structure Cluster, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
    For correspondence
    gerard@ebi.ac.uk
    Competing interests
    No competing interests declared.

Funding

Medical Research Council (MR/L007835)

  • Gerard J Kleywegt

European Commission (284209)

  • Gerard J Kleywegt

Wellcome (104948)

  • Gerard J Kleywegt

National Institutes of Health (R01 GM079429)

  • Gerard J Kleywegt

Medical Research Council (MR/N009614/1)

  • Martyn Winn

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Werner Kühlbrandt, Max Planck Institute of Biophysics, Germany

Publication history

  1. Received: February 8, 2017
  2. Accepted: June 30, 2017
  3. Accepted Manuscript published: July 6, 2017 (version 1)
  4. Version of Record published: July 24, 2017 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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