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Towards an efficient compression of 3D coordinates of macromolecular structures

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Listed:
  • Yana Valasatava
  • Anthony R Bradley
  • Alexander S Rose
  • Jose M Duarte
  • Andreas Prlić
  • Peter W Rose

Abstract

The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

Suggested Citation

  • Yana Valasatava & Anthony R Bradley & Alexander S Rose & Jose M Duarte & Andreas Prlić & Peter W Rose, 2017. "Towards an efficient compression of 3D coordinates of macromolecular structures," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-15, March.
    • Handle: RePEc:plo:pone00:0174846
    DOI: 10.1371/journal.pone.0174846
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    References listed on IDEAS

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    1. Daniel Russel & Keren Lasker & Ben Webb & Javier Velázquez-Muriel & Elina Tjioe & Dina Schneidman-Duhovny & Bret Peterson & Andrej Sali, 2012. "Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies," PLOS Biology, Public Library of Science, vol. 10(1), pages 1-5, January.
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