Evidence map›Paper›PMID 31603581›Full record

ArticleProteins2019

Protein structure prediction assisted with sparse NMR data in CASP13.

Davide Sala, Yuanpeng Janet Huang, Casey A Cole, David A Snyder, Gaohua Liu, Yojiro Ishida, G V T Swapna, Kelly P Brock, Chris Sander, Krzysztof Fidelis and 6 more

Abstract read
In one paragraph

Article in Proteins, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2023
    Article
  5. Article
  6. Article
  7. Conformational ensemble of the TNF-derived peptide solnatide in solution.Computational and structural biotechnology journal · 2022
    Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Protein storytelling through physics.Science (New York, N.Y.) · 2020
    Review
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

16 authors.

Davide SalaMagnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy.ORCID 0000-0002-3900-0011
Yuanpeng Janet HuangCenter for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
Casey A ColeDepartment of Computer Science & Engineering, University of South Carolina, Columbia, South Carolina.
David A SnyderDepartment of Chemistry, College of Science and Health, William Paterson University, Wayne, New Jersey.ORCID 0000-0001-6608-2975
Gaohua LiuCenter for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
Yojiro IshidaCenter for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
G V T SwapnaCenter for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
Kelly P BrockDepartment of Systems Biology, Harvard Medical School, Boston, Massachusetts.
Chris SanderDepartment of Cell Biology, Harvard Medical School, Boston, Massachusetts.
Krzysztof FidelisGenome Center, University of California, Davis, California.ORCID 0000-0002-8061-412X
Andriy KryshtafovychGenome Center, University of California, Davis, California.ORCID 0000-0001-5066-7178
Masayori InouyeDepartment of Biochemistry and Molecular Biology, The Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
Roberto TejeroDepartamento de Quimica Fisica, Universidad de Valencia, Valencia, Spain.
Homayoun ValafarDepartment of Computer Science & Engineering, University of South Carolina, Columbia, South Carolina.
Antonio RosatoMagnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy.ORCID 0000-0001-6172-0368
Gaetano T MontelioneCenter for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey.ORCID 0000-0002-9440-3059

Funding

Supplement for South Carolina BRIN - 1P20 RR16461P20RR016461 · NCRR · UNIVERSITY OF SOUTH CAROLINA AT COLUMBIA · PI DEAVOR, JAMES · 2001 to 2011
$32.3M
Prospective analysis to determine model accuracy performance and boundaries in the post-AlphaFold2 environmentR01GM100482 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI FIDELIS, KRZYSZTOF A · 2012 to 2025
$11.1M
Membrane Protein Structure Using Evolutionary Couplings and Sparse NMR DataR01GM120574 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI MONTELIONE, GAETANO T · 2017 to 2020
$2.3M
600 MHZ NMR RF Console with 19F NMR ProbeS10OD018207 · OD · RUTGERS, THE STATE UNIV OF N.J. · PI MONTELIONE, GAETANO T · 2014 to 2014
$440k
NCRR NIH HHS P20 RR016461NIGMS NIH HHS 1R01GM120574NIGMS NIH HHS R01 GM100482NIGMS NIH HHS R01GM100482NIGMS NIH HHS R01 GM120574NIH HHS P20 RR-016461NIH HHS S10 OD018207
6 · The paper itself

Abstract

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and

Indexed as

Models, MolecularProtein ConformationProtein FoldingAlgorithmsComputer SimulationCrystallography, X-RayMagnetic Resonance SpectroscopyProteinsReproducibility of ResultsProteinsCASPcontact predictionprotein modelingresidual dipolar couplingsimulated NMR spectrasparse NMR datastructure prediction

Identifiers

PMID31603581
PMCPMC7213643

What OpenQuestion holds

Textmetadata
LicenceTDM
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.