Evidence map›Paper›PMID 40092446›Full record

ArticleResearch square2025

Deconvolution to restore cryo-EM maps with anisotropic resolution.

Yifan Cheng, Junrui Li, Yifei Chen, Shawn Zheng, Angus McDonald, John Sedat, David Agard

Abstract readPreprint
In one paragraph

Article in Research square, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Yifan ChengHHMI/University of California San Francisco.ORCID 0000-0001-9535-0369
Junrui LiHoward Hughes Medical Institute.
Yifei ChenHoward Hughes Medical Institute.
Shawn ZhengChan Zuckerberg Imaging Institute.
Angus McDonaldMicron School of Material Science and Engineering, Boise State University.
John SedatUniv. Calif. San Francisco.
David AgardUniversity of California San Francisco.ORCID 0000-0003-3512-695X

Funding

Project 3U54AI170792 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nevan J Krogan · 2022 to 2026
$35.7M
Advancing cryo-EM technology to address difficult biological questionsR35GM140847 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Yifan Cheng · 2021 to 2026
$2.1M
Acquisition of an electron microscope for high-resolution single particle cryo-EMS10OD021741 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2016 to 2016
$2.0M
Linux cluster for near atomic resolution single particle cryo-EMS10OD020054 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2015 to 2015
$456k
NIAID NIH HHS U54 AI170792NIGMS NIH HHS R35 GM140847NIH HHS S10 OD020054NIH HHS S10 OD021741
6 · The paper itself

Abstract

With technological advancements in recent years, single particle cryogenic electron microscopy (cryo-EM) has become a major methodology for structural biology. Structure determination by single particle cryo-EM is premised on randomly orientated particles embedded in thin layer of vitreous ice to resolve high-resolution structural information in all directions. Otherwise, preferentially distributed particle orientations will lead to anisotropic resolution of the structure. Here we established a deconvolution approach, named AR-Decon, to computationally improve the quality of three-dimensional maps with anisotropic resolutions reconstructed from datasets with preferred orientations. We have tested and validated the procedure with both synthetic and experimental datasets and compared its performance with alternative machine-learning based methods.

Identifiers

PMID40092446
PMCPMC11908346

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.