Deepsharpen: Deep-Learning Based Sharpening of 3D Reconstruction Map from Cryo-Electron Microscopy

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Cryo-electron microscopy (cryo-EM) has proven to be a promising tool for recovering the 3D structure of biological macromolecules. The cryo-EM map which is reconstructed from a large set of projection images, is then used for recovering the atomic model of the molecule. The accuracy of the fitted atomic model depends on the quality of the cryo-EM map. Due to current limitations during imaging or reconstruction process, the reconstructed map usually lacks interpretability and requires further quality enhancement post-processing. In this work, we present a data-driven solution to improve the quality of low-resolution cryo-EM maps. For this purpose, we generate a synthetic dataset generated from deposited protein structures in protein data bank (PDB). This dataset includes low and high-resolution map pairs in multiple resolutions. This dataset is then used to train a fully convolutional network. Our results justify the potential of our method in successfully recovering details for simulated and experimental maps. Moreover, compared to state-of-the-art cryo-EM map sharpening methods, our approach not only provides good results but is also computationally efficient.

Original languageEnglish (US)
Title of host publicationISBI Workshops 2020 - International Symposium on Biomedical Imaging Workshops, Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781728174013
DOIs
StatePublished - Apr 2020
Event17th IEEE International Symposium on Biomedical Imaging Workshops, ISBI Workshops 2020 - Iowa City, United States
Duration: Apr 4 2020 → …

Publication series

NameISBI Workshops 2020 - International Symposium on Biomedical Imaging Workshops, Proceedings

Conference

Conference17th IEEE International Symposium on Biomedical Imaging Workshops, ISBI Workshops 2020
CountryUnited States
CityIowa City
Period4/4/20 → …

Keywords

  • cryo-EM
  • density map sharpening
  • local resolution
  • post-processing
  • protein data bank

ASJC Scopus subject areas

  • Signal Processing
  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

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