Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)

Abstract

Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations.

Original languageEnglish
Pages (from-to)172-181
Number of pages10
JournalJournal of Structural Biology
Volume204
Issue number2
DOIs
Publication statusPublished - Nov 2018

Keywords

  • 3D reconstruction
  • cryo-EM
  • Electron microscopy
  • Image processing
  • Near-atomic resolution
  • Single-particle
  • Stochastic hill-climbing

Cite this

@article{d0e91b6aa1c54519b613853a746713f5,
title = "Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE",
abstract = "Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations.",
keywords = "3D reconstruction, cryo-EM, Electron microscopy, Image processing, Near-atomic resolution, Single-particle, Stochastic hill-climbing",
author = "Reboul, {Cyril F.} and Simon Kiesewetter and Michael Eager and Matthew Belousoff and Tiangang Cui and {De Sterck}, Hans and Dominika Elmlund and Hans Elmlund",
year = "2018",
month = "11",
doi = "10.1016/j.jsb.2018.08.005",
language = "English",
volume = "204",
pages = "172--181",
journal = "Journal of Structural Biology",
issn = "1047-8477",
publisher = "Elsevier",
number = "2",

}

Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE. / Reboul, Cyril F.; Kiesewetter, Simon; Eager, Michael; Belousoff, Matthew; Cui, Tiangang; De Sterck, Hans; Elmlund, Dominika; Elmlund, Hans.

In: Journal of Structural Biology, Vol. 204, No. 2, 11.2018, p. 172-181.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE

AU - Reboul, Cyril F.

AU - Kiesewetter, Simon

AU - Eager, Michael

AU - Belousoff, Matthew

AU - Cui, Tiangang

AU - De Sterck, Hans

AU - Elmlund, Dominika

AU - Elmlund, Hans

PY - 2018/11

Y1 - 2018/11

N2 - Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations.

AB - Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations.

KW - 3D reconstruction

KW - cryo-EM

KW - Electron microscopy

KW - Image processing

KW - Near-atomic resolution

KW - Single-particle

KW - Stochastic hill-climbing

UR - http://www.scopus.com/inward/record.url?scp=85051372005&partnerID=8YFLogxK

U2 - 10.1016/j.jsb.2018.08.005

DO - 10.1016/j.jsb.2018.08.005

M3 - Article

VL - 204

SP - 172

EP - 181

JO - Journal of Structural Biology

JF - Journal of Structural Biology

SN - 1047-8477

IS - 2

ER -