Evidence map›Paper›PMID 31588918›Full record

ArticleActa crystallographica. Section D, Structural biology2019

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy and 15 more

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Structural biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4,592 papers.

0numbers the graph read from it
0cells of the map it votes in
4,592citing 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

4,592 citing papers in PubMed.

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  17. DNAAF19-RUVBL1/2 complex recruits multiple adaptors to promote dynein arm assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026
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  19. Mechanisms of intracellular pH gating and local anesthetic inhibition of the two-pore domain KProceedings of the National Academy of Sciences of the United States of America · 2026
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  20. Article

4,532 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors.

Dorothee LiebschnerMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0003-3921-3209
Pavel V AfonineMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-5052-991X
Matthew L BakerVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Gábor BunkócziDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.
Vincent B ChenDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
Tristan I CrollDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.
Bradley HintzeDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.ORCID 0000-0002-4871-2096
Li Wei HungLos Alamos National Laboratory, Los Alamos, NM 87545, USA.ORCID 0000-0001-6690-8458
Swati JainDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
Airlie J McCoyDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.
Nigel W MoriartyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-8857-9464
Robert D OeffnerDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.ORCID 0000-0003-3107-2202
Billy K PoonMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-9633-6067
Michael G PrisantDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
Randy J ReadDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.ORCID 0000-0001-8273-0047
Jane S RichardsonDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
David C RichardsonDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
Massimo D SammitoDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.
Oleg V SobolevMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-0623-3214
Duncan H StockwellDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England.
Thomas C TerwilligerLos Alamos National Laboratory, Los Alamos, NM 87545, USA.ORCID 0000-0001-6384-0320
Alexandre G UrzhumtsevCentre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 67404 Illkirch, France.
Lizbeth L VideauDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
Christopher J WilliamsDepartment of Biochemistry, Duke University, Durham, NC 27710, USA.
Paul D AdamsMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-9333-8219

Funding

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
Computational Tools for Neutron Protein CrystallographyR01GM071939 · NIGMS · UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB · PI COATES, LEIGHTON · 2004 to 2019
$4.3M
NIGMS NIH HHS P01 GM063210NIGMS NIH HHS R01 GM071939NIH HHS 1R01GM071939NIH HHS P01GM063210Wellcome TrustWellcome Trust 209407/Z/17/Z
6 · The paper itself

Abstract

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

Indexed as

Software DesignSoftware ValidationAutomationCryoelectron MicroscopyCrystallography, X-RayMacromolecular SubstancesModels, MolecularMolecular ConformationMacromolecular SubstancesautomationC++cctbxcryo-EMdiffractionmacromolecular crystallographyneutronsPhenixPythonX-rays

Identifiers

PMID31588918
PMCPMC6778852

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.