Evidence map›Paper›PMID 26280328›Full record

ArticleNature methods2015

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser

Abstract read
In one paragraph

Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 655 papers.

0numbers the graph read from it
0cells of the map it votes in
655citing 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

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

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

655 citing papers in PubMed.

  1. Article
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  3. The structural basis of malodorant skatole formation by the glycyl radical enzyme indoleacetate decarboxylase.Proceedings of the National Academy of Sciences of the United States of America · 2026
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595 more citing papers are in PubMed but not listed here.

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.

Benjamin A BaradDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.ORCID http://orcid.org/0000-0002-1016-862X
Nathaniel EcholsPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Ray Yu-Ruei WangGraduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, USA.
Yifan ChengKeck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA.
Frank DiMaioDepartment of Biochemistry, University of Washington, Seattle, Washington, USA.
Paul D AdamsPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.ORCID http://orcid.org/0000-0002-5080-2859

Funding

X-ray Screening and Rapid Structure DeterminationP50GM082250 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRANKEL, ALAN D · 2007 to 2018
$48.8M
PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5M
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
Integrative Program in Complex Biological System (ipCBS)T32EB009383 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MARSHALL, WALLACE, WEINER, ORION D · 2009 to 2022
$3.2M
Mechanism of gate-opening in the 20S proteasome induced by the proteasomal ATPaseR01GM082893 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2008 to 2017
$2.8M
Structures and gating mechanisms of TRP ion channelsR01GM098672 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2011 to 2018
$2.6M
The Impact of Mutation on the Conformations and Recognition of UbiquitinDP5OD009180 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRASER, JAMES SOLOMON · 2011 to 2015
$1.8M
Model Comparison in Structural BiologyR21GM110580 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRASER, JAMES SOLOMON · 2014 to 2015
$419k
NIBIB NIH HHS T32 EB009383NIGMS NIH HHS GM063210NIGMS NIH HHS GM082250NIGMS NIH HHS GM082893NIGMS NIH HHS GM098672NIGMS NIH HHS GM110580NIGMS NIH HHS P01 GM063210NIGMS NIH HHS P50 GM082250NIGMS NIH HHS R01 GM082893NIGMS NIH HHS R01 GM098672NIGMS NIH HHS R21 GM110580NIGMS NIH HHS T32 GM008284NIGMS NIH HHS T32GM008284NIH HHS DP5 OD009180NIH HHS OD009180
6 · The paper itself

Abstract

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

Indexed as

SoftwareCryoelectron MicroscopyCrystallography, X-RayDatabases, ProteinImage Processing, Computer-AssistedModels, MolecularProtein ConformationProteinsReproducibility of ResultsTRPV Cation ChannelsProteinsTrpv1 protein, ratTRPV Cation Channels

Identifiers

PMID26280328
PMCPMC4589481

What OpenQuestion holds

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Registered trials

None linked

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.