TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis

Structure. 2017 Jun 6;25(6):951-961.e2. doi: 10.1016/j.str.2017.04.016. Epub 2017 May 25.

Abstract

Cryo-electron tomography (cryo-ET) captures the 3D electron density distribution of macromolecular complexes in close to native state. With the rapid advance of cryo-ET acquisition technologies, it is possible to generate large numbers (>100,000) of subtomograms, each containing a macromolecular complex. Often, these subtomograms represent a heterogeneous sample due to variations in the structure and composition of a complex in situ form or because particles are a mixture of different complexes. In this case subtomograms must be classified. However, classification of large numbers of subtomograms is a time-intensive task and often a limiting bottleneck. This paper introduces an open source software platform, TomoMiner, for large-scale subtomogram classification, template matching, subtomogram averaging, and alignment. Its scalable and robust parallel processing allows efficient classification of tens to hundreds of thousands of subtomograms. In addition, TomoMiner provides a pre-configured TomoMinerCloud computing service permitting users without sufficient computing resources instant access to TomoMiners high-performance features.

Keywords: cloud computing; cryo-electron tomography; distributed computing; fast rotational matching; subtomogram alignment; subtomogram classification.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chaperonin 10 / chemistry
  • Chaperonin 60 / chemistry
  • Cloud Computing / economics
  • Clusterin
  • Electron Microscope Tomography / methods*
  • Image Processing, Computer-Assisted / methods
  • Software*

Substances

  • Chaperonin 10
  • Chaperonin 60
  • Clusterin