Evidence map›Paper›PMID 38490206›Full record

ArticleStructure (London, England : 1993)2024

Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.

Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Structure (London, England : 1993), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026
    Article
  3. Article
  4. Associating protein residues in the literature with structural data.Acta crystallographica. Section D, Structural biology · 2026
    Article
  5. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Kumaran BaskaranBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA. Electronic address: baskaran@uchc.edu.
Eliza PloskonDepartment of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK.
Roberto TejeroDepartamento de Quίmica Fίsica, Universidad de Valencia, Dr. Moliner, 50 46100 Burjassot, Valencia, Spain.
Masashi YokochiProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; Protein Data Bank Japan, Protein Research Foundation, Minoh, Osaka 562-8686, Japan.
Deborah HarrusProtein Data Bank in Europe, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Yuhe LiangResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Ezra PeisachResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Irina PersikovaResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Theresa A RamelotDepartment of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
Monica SekharanResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
James TolchardProtein Data Bank in Europe, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
John D WestbrookResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Benjamin BardiauxDepartment of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3528, 75015 Paris, France.
Charles D SchwietersComputational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
Ardan PatwardhanThe Electron Microscopy Data Bank, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Sameer VelankarProtein Data Bank in Europe, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, La Jolla, CA, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Genji KurisuProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; Protein Data Bank Japan, Protein Research Foundation, Minoh, Osaka 562-8686, Japan.
Jeffrey C HochBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
Gaetano T MontelioneDepartment of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA. Electronic address: monteg3@rpi.edu.
Geerten W VuisterDepartment of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK. Electronic address: gv29@leicester.ac.uk.
Jasmine Y YoungResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address: jasmin@rcsb.rutgers.edu.

Funding

PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3M
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
The BMRB as an evolving resource for biomolecular structure-function researchR01GM109046 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI HOCH, JEFFREY C · 2014 to 2022
$6.6M
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 GM109046NIGMS NIH HHS R01 GM133198NIGMS NIH HHS R01 GM157729NIGMS NIH HHS R24 GM150793NIGMS NIH HHS R35 GM141818Wellcome Trust
6 · The paper itself

Abstract

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB restraint violation report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

Indexed as

Databases, ProteinModels, MolecularNuclear Magnetic Resonance, BiomolecularProtein ConformationProteinsSoftwareProteinsbiomolecular structuresdata standarddihedral-angle restraintsdistance restraintsNMRNMR exchange formatNMR-STARProtein Data Bankrestraint violationvalidation

Identifiers

PMID38490206
PMCPMC11162339

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.