Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER
File(s)
Published version
Author(s)
Ramlaul, Kailash
Palmer, Colin
Nakane, Takanori
Aylett, Christopher
Type
Journal Article
Abstract
Single particle analysis has become a key structural biology technique. Experimental images are extremely noisy, and during iterative refinement it is possible to stably incorporate noise into the reconstruction. Such “over-fitting” can lead to misinterpretation of the structure and flawed biological results. Several strategies are routinely used to prevent over-fitting, the most common being independent refinement of two sides of a split dataset. In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise, despite independent refinement of half datasets. We propose a modification of the refinement process through the application of a local signal-to-noise filter: SIDESPLITTER. We show that our approach can reduce over-fitting for both idealised and experimental data while maintaining independence between the two sides of a split refinement. SIDESPLITTER refinement leads to improved density, and can also lead to improvement of the final resolution in extreme cases where datasets are prone to severe over-fitting, such as small membrane proteins.
Date Issued
2020-08
Date Acceptance
2020-06-02
Citation
Journal of Structural Biology, 2020, 211 (2), pp.1-9
ISSN
1047-8477
Publisher
Elsevier
Start Page
1
End Page
9
Journal / Book Title
Journal of Structural Biology
Volume
211
Issue
2
Copyright Statement
© 2020 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/BY/4.0/).
License URL
Sponsor
Wellcome Trust
Identifier
https://www.sciencedirect.com/science/article/pii/S1047847720301180?via%3Dihub
Grant Number
206212/Z/17/Z
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Biophysics
Cell Biology
Cryo-EM
Local resolution
Noise suppression
Real-space filter
Over-fitting
CRYO-EM
ELECTRON-MICROSCOPY
CRYOELECTRON MICROSCOPY
RESOLUTION
REFINEMENT
IMPLEMENTATION
ORIENTATION
Cryo-EM
Local resolution
Noise suppression
Over-fitting
Real-space filter
0601 Biochemistry and Cell Biology
0608 Zoology
Biophysics
Publication Status
Published
Date Publish Online
2020-06-10