Matching of EM Map Segments to Structurally-Relevant Bio-molecular Regions

  • Manuel Zumbado-Corrales
  • Luis Castillo-Valverde
  • José Salas-Bonilla
  • Julio Víquez-Murillo
  • Daisuke Kihara
  • Juan Esquivel-RodríguezEmail author
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 1087)


Electron microscopy is a technique used to determine the structure of bio-molecular machines via three-dimensional images (called maps). The state-of-the-art is able to determine structures at resolutions that allow us to identify up to secondary structural features, in some cases, but it is not widespread. Furthermore, because molecular interactions often require atomic-level details to be understood, it is still necessary to complement current maps with techniques that provide finer-grain structural details. We applied segmentation techniques to maps in the Electron Microscopy Data Bank (EMDB), the standard community repository for these data. We assessed the potential of these algorithms to match functionally relevant regions in their atomic-resolution image counterparts by comparing against three protein systems, each with multiple atomic-detailed domains. We found that at least 80% of amino acid residues in 7 out of 12 domains were assigned to single segments, suggesting there is potential to match the lower resolution segmented regions to the atomic counterparts. We also qualitatively analyzed the potential on other EMDB structures, as well as generating the raw segmentation information for the complete EMDB, for interested researchers to use. Results can be accessed online and the library developed is provided as part of an open-source project.


Computational biology Computational protein structures Electron microscopy 3DEM Segmentation 



Funded by the Vicerrrectoría de Investigación y Extensión at Instituto Tecnológico de Costa Rica.


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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Manuel Zumbado-Corrales
    • 1
    • 2
  • Luis Castillo-Valverde
    • 1
  • José Salas-Bonilla
    • 1
  • Julio Víquez-Murillo
    • 1
  • Daisuke Kihara
    • 3
  • Juan Esquivel-Rodríguez
    • 1
    Email author
  1. 1.Instituto Tecnológico de Costa Rica, Escuela de ComputaciónCartagoCosta Rica
  2. 2.Advanced Computing LaboratoryNational High Technology CenterSan JoséCosta Rica
  3. 3.Department of Biological Sciences/Department of Computer SciencePurdue UniversityWest LafayetteUSA

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