Evidence map›Paper›PMID 28573593›Full record

ReviewMethods in molecular biology (Clifton, N.J.)2017

Databases, Repositories, and Other Data Resources in Structural Biology.

Heping Zheng, Przemyslaw J Porebski, Marek Grabowski, David R Cooper, Wladek Minor

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Methods in molecular biology (Clifton, N.J.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. 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

5 authors.

Heping ZhengDepartment of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA.
Przemyslaw J PorebskiDepartment of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA.
Marek GrabowskiDepartment of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA.
David R CooperDepartment of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA.
Wladek MinorDepartment of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA. wladek@iwonka.med.virginia.edu.

Funding

X-RAY CRYSTALLOGRAPHY OF MACROMOLECULESR01GM053163 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 1996 to 2014
$6.3M
Integrated resource for reproducibility in macromolecular crystallographyU01HG008424 · NHGRI · UNIVERSITY OF VIRGINIA · PI MINOR, WLADEK · 2015 to 2017
$1.5M
X-ray data analysis in the presence of structural variability - Administrative SupplementR01GM117080 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 2015 to 2018
$1.4M
Metal binding sites in macromolecular structuresR01GM117325 · NIGMS · UNIVERSITY OF VIRGINIA · PI MINOR, WLADEK · 2016 to 2019
$1.3M
NHGRI NIH HHS U01 HG008424NIAID NIH HHS HHSN272201200026CNIGMS NIH HHS R01 GM053163NIGMS NIH HHS R01 GM117080NIGMS NIH HHS R01 GM117325
6 · The paper itself

Abstract

Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

Indexed as

Computational BiologyCrystallography, X-RayDatabases, ProteinInformation Storage and RetrievalInternetMacromolecular SubstancesMicroscopy, ElectronModels, MolecularProtein ConformationProteinsSoftwareStereoisomerismMacromolecular SubstancesProteinsArchiveDatabaseData resourceInformation systemMetadataRepositoryStructural biology

Identifiers

PMID28573593
PMCPMC5587190

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.