Evidence map›Paper›PMID 42079120›Full record

ArticlebioRxiv : the preprint server for biology2026

The NMR Exchange Format (NEF): Specification and Applications.

Eliza Płoskoń, Kumaran Baskaran, Roberto Tejero, Charles D Schwieters, Benjamin Bardiaux, Peter Guentert, Rasmus H Fogh, Aleksandras Gutmanas, Edward J Brooksbank, Masashi Yokochi and 32 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

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

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

42 authors.

Eliza PłoskońDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0009-0006-1863-4345
Kumaran BaskaranBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT-06030, USA.ORCID 0000-0002-0418-0286
Roberto TejeroDepartamento Química Física. Universidad de Valencia. Avda Dr. Moliner, 50. Burjassot (Valencia). Spain.ORCID 0000-0003-2504-5988
Charles D SchwietersLaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.ORCID 0000-0002-4216-4658
Benjamin BardiauxBacterial Transmembrane Systems Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3528, 75015, Paris, France.ORCID 0000-0003-4014-9195
Peter GuentertInstitute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland.ORCID 0000-0002-2911-7574
Rasmus H FoghDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0009-0000-6340-7754
Aleksandras GutmanasProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.ORCID 0000-0001-6311-0176
Edward J BrooksbankDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0009-0008-1721-7405
Masashi YokochiProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.ORCID 0000-0002-3253-7449
David S WishartDepartment of Biological Sciences, CW 405, Biological Sciences Building, University of Alberta, Edmonton, Alberta, Canada T6G 2E9.ORCID 0000-0002-3207-2434
Jonathan R WedellBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT-06030, USA.ORCID 0000-0002-2247-6259
Wim F VrankenInteruniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, 1050, Belgium.ORCID 0000-0001-7470-4324
Daniel ThompsonDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0009-0006-6436-6580
Gary ThomsonWellcome Biomolecular NMR Facility, School of Natural Sciences, University of Kent, Canterbury, CT2 7NZ, United Kingdom.ORCID 0000-0001-9399-7636
Brian O SmithSchool of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Joseph Black Building, University of Glasgow, G12 8QQ, United Kingdom.ORCID 0000-0003-3363-4168
Saima RehmanCentre for Host-Microbiome Interactions, King's College London, London, SE1 9RT, UK.ORCID 0000-0001-9552-0575
Theresa A RamelotDepartment of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.ORCID 0000-0002-0335-1573
Timothy J RaganDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0000-0002-6233-3375
Alberto PerezDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32607, USA.ORCID 0000-0002-5054-5338
Binod L PereraDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32607, USA.
Ezra PeisachRCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.ORCID 0000-0002-7905-6327
Michael NilgesStructural Bioinformatics Unit, Institut Pasteur, Université Paris-Cité, CNRS UMR3528, 75015, Paris, France.ORCID 0000-0002-1451-8092
Luca G MuredduDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0000-0002-7008-484X
Arup MondalDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32607, USA.ORCID 0000-0002-8970-3380
Emilia A LubeckaGdańsk University of Technology, Faculty of Electronics, Telecommunications and Informatics, G. Narutowicza 11/12, 80-233 Gdańsk, Poland.ORCID 0000-0003-2590-7269
Adam LiwoFaculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.ORCID 0000-0001-6942-2226
Genji KurisuProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.ORCID 0000-0002-5354-0807
Naohiro KobayashiProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.ORCID 0000-0001-5136-2077
Piotr KlukowskiInstitute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland.ORCID 0000-0003-1045-3487
Bruce A JohnsonStructural Biology Initiative, Advanced Science Research Center at the CUNY Graduate Center, New York, NY, USA.ORCID 0000-0001-8445-5368
Yuanpeng J HuangDepartment of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.ORCID 0000-0002-3374-786X
Jeffrey C HochBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT-06030, USA.ORCID 0000-0002-9230-2019
Victoria A HigmanDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0000-0002-3204-2665
Torsten HerrmannUniversity Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.ORCID 0000-0003-2115-4781
Morgan W HaywardDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0009-0003-3200-4874
James A GarnettCentre for Host-Microbiome Interactions, King's College London, London, SE1 9RT, UK.ORCID 0000-0001-7621-8223
David A CaseDepartment of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.ORCID 0000-0003-2314-2346
Stephen K BurleyRCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.ORCID 0000-0002-2487-9713
Paul D AdamsMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0001-9333-8219
Gaetano T MontelioneDepartment of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.ORCID 0000-0002-9440-3059
Geerten W VuisterDivision of Molecular and Cellular Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, United Kingdom.ORCID 0000-0001-6172-5097

Funding

PDB Management by the Research Collaboratory for Structural BioinformaticsR01GM157729 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI STEPHEN K BURLEY · 2024 to 2026
$11.6M
Hybrid Methods for Dynamic Structure Analysis of Proteins from Pathogenic MicroorganismsR35GM141818 · NIGMS · RENSSELAER POLYTECHNIC INSTITUTE · PI MONTELIONE, GAETANO T · 2021 to 2025
$3.3M
Biological Magnetic Resonance Data BankR24GM150793 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI JEFFREY C HOCH · 2023 to 2026
$3.0M
NIGMS NIH HHS R01 GM157729NIGMS NIH HHS R24 GM150793NIGMS NIH HHS R35 GM141818
6 · The paper itself

Abstract

The NMR Exchange Format (NEF) is a community-driven standard for representing NMR experimental data in a consistent, interoperable, and machine-readable form. Built on the STAR syntax, NEF provides a structured framework for storing and exchanging chemical shifts, peak lists, various types of structural restraints, and related metadata, thus allowing for data exchange across software platforms. By enabling direct, lossless transfer of information, NEF simplifies multi-software workflows, improves reproducibility, and supports FAIR (Findable, Accessible, Interoperable, Reusable) data principles. We describe the NEF specification, its current implementation across commonly used NMR software packages, and its application in areas including biomolecular structure determination, metabolomics, and ligand screening. Testing demonstrates that NEF can be used to exchange complete datasets between programs without loss of information or functionality. We also outline recent developments and future directions, such as inclusion of NMR relaxation data and support for non-standard residue topologies. NEFs growing adoption highlights its potential as a unifying standard for NMR data, enabling more efficient, transparent and collaborative research.

Identifiers

PMID42079120
PMCPMC13131792

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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.