Evidence map›Paper›PMID 40326523›Full record

ArticleNucleic acids research2025

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations.

Adam Midlik, Sebastian Bittrich, Jennifer R Fleming, Sreenath Nair, Sameer Velankar, Stephen K Burley, Jasmine Y Young, Brinda Vallat, David Sehnal

Abstract read
In one paragraph

Article in Nucleic acids research, 2025. 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. Article
  3. MolViewStories: Interactive molecular storytelling.Protein science : a publication of the Protein Society · 2026
    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

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

9 authors.

Adam MidlikProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0003-0455-2235
Sebastian BittrichResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, United States.ORCID 0000-0003-3576-0387
Jennifer R FlemingProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0003-4016-8740
Sreenath NairProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0002-6861-7627
Sameer VelankarProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0002-8439-5964
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, United States.ORCID 0000-0002-2487-9713
Jasmine Y YoungResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.ORCID 0000-0001-8896-6878
Brinda VallatResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.
David SehnalProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.

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
Czech Republic JuniorStar project 22-30571MEMBL-EBIMasaryk UniversityNational Institute of Allergy and Infectious DiseasesNational Science FoundationNCI NIH HHSNIGMS NIH HHS R01 GM157729NIH HHS R01GM157729NSF DBI-2321666UK Biotechnology and Biological Research Council BB/W017970/1UK Biotechnology and Biological Research Council DBI-2129634United States Department of Energy DE-SC0019749
6 · The paper itself

Abstract

Data visualization is a pivotal component of a structural biologist's arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Indexed as

Computer GraphicsSoftwareInternetUser-Computer Interface

Identifiers

PMID40326523
PMCPMC12230705

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.