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 language | English |
|---|---|
| Pages (from-to) | 172-181 |
| Number of pages | 10 |
| Journal | Journal of Structural Biology |
| Volume | 204 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - Nov 2018 |
Keywords
- 3D reconstruction
- cryo-EM
- Electron microscopy
- Image processing
- Near-atomic resolution
- Single-particle
- Stochastic hill-climbing
Cite this
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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 journal › Article › Research › peer-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 -