Evidence map›Paper›PMID 27450113›Full record

ReviewCurrent opinion in structural biology2016

The archiving and dissemination of biological structure data.

Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar

Abstract readReview
In one paragraph

Review in Current opinion in structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing 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

20 citing papers in PubMed.

  1. Article
  2. Review
  3. Computational Resources for the Interpretation of Variations in Cancer.Advances in experimental medicine and biology · 2022
    Article
  4. Article
  5. Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.Methods in molecular biology (Clifton, N.J.) · 2021
    Review
  6. Article
  7. Review
  8. Nucleobase carbonyl groups are poor MgRNA (New York, N.Y.) · 2019
    Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Where is crystallography going?Acta crystallographica. Section D, Structural biology · 2018
    Review
  15. New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).Protein science : a publication of the Protein Society · 2018
    Article
  16. Article
  17. Article
  18. Article
  19. Biocuration in the structure-function linkage database: the anatomy of a superfamily.Database : the journal of biological databases and curation · 2017
    Article
  20. Article
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

6 authors.

Helen M BermanResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA. Electronic address: berman@rcsb.rutgers.edu.
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Gerard J KleywegtProtein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.
John L MarkleyBiological Magnetic Resonance Bank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Haruki NakamuraProtein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Sameer VelankarProtein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK.

Funding

Unified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$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
Biotechnology and Biological Sciences Research Council BB/J007471/1Biotechnology and Biological Sciences Research Council BB/K016970/1Biotechnology and Biological Sciences Research Council BB/K020013/1Biotechnology and Biological Sciences Research Council BB/M011674/1Biotechnology and Biological Sciences Research Council BB/M013146/1Biotechnology and Biological Sciences Research Council BB/M020347/1Biotechnology and Biological Sciences Research Council BB/M020428/1Medical Research Council MR/L007835/1NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM109046Wellcome TrustWellcome Trust 104948
6 · The paper itself

Abstract

The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.

Indexed as

Databases, ProteinData CurationHumans

Identifiers

PMID27450113
PMCPMC5161703

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.