Evidence map›Paper›PMID 34655449›Full record

ArticleProtein science : a publication of the Protein Society2022

SMOG 2 and OpenSMOG: Extending the limits of structure-based models.

Antonio B de Oliveira, Vinícius G Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, Esteban Dodero-Rojas, Udayan Mohanty, Jeffrey K Noel, Jose N Onuchic and 1 more

Open access · greenAbstract read
In one paragraph

Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
9.0field-weighted citation impact, top 3% of its field
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

18 citing papers in PubMed, 39 citations in OpenAlex.

  1. Article
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  5. Exploring functional transitions of the 2'-dG riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2026
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  7. Ribosomal Protein bL27 Protects Translating Ribosomes from tmRNA-SmpB.bioRxiv : the preprint server for biology · 2026
    Article
  8. Article
  9. Article
  10. Article
  11. Mapping the energy landscape of a fold-switching protein MAD2.Protein science : a publication of the Protein Society · 2025
    Article
  12. Article
  13. Simulating biomolecules for physiological timescales.Current opinion in structural biology · 2025
    Review
  14. Article
  15. Article
  16. Article
  17. Review
  18. SMOG 2 and OpenSMOG: Extending the limits of structure-based models.Protein science : a publication of the Protein Society · 2022
    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

11 authors at 4 institutions in 2 countries.

Antonio B de OliveiraCenter for Theoretical Biological Physics, Rice University, Houston, Texas, USA.ORCID 0000-0003-1955-3556
Vinícius G ContessotoCenter for Theoretical Biological Physics, Rice University, Houston, Texas, USA.ORCID 0000-0002-1891-9563
Asem HassanDepartment of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, USA.ORCID 0000-0003-0220-195X
Sandra ByjuDepartment of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, USA.
Ailun WangCenter for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA.ORCID 0000-0002-4214-2352
Yang WangDepartment of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA.
Esteban Dodero-RojasCenter for Theoretical Biological Physics, Rice University, Houston, Texas, USA.ORCID 0000-0001-9054-9555
Udayan MohantyDepartment of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA.ORCID 0000-0002-8778-974X
Jeffrey K NoelCrystallography, Max Delbrück Center for Molecular Medicine, Berlin, Germany.ORCID 0000-0003-3168-6036
Jose N OnuchicCenter for Theoretical Biological Physics, Rice University, Houston, Texas, USA.ORCID 0000-0002-9448-0388
Paul C WhitfordDepartment of Physics, Northeastern University, Dana Research Center, Boston, Massachusetts, USA.ORCID 0000-0001-7104-2265
Center for Theoretical Biological Physics · USNortheastern University · USBoston College · USMax Delbrück Center · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Applying simulations with structure-based

Indexed as

Molecular Dynamics SimulationSoftwareAnimalsCOVID-19HumansModels, MolecularProtein ConformationProteinsRibosomesSARS-CoV-2Spike Glycoprotein, CoronavirusProteinsSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2assembliesDNAenergy landscapeproteinRNAsimulation

Identifiers

PMID34655449
PMCPMC8740843
OpenAlexW3207327265

What OpenQuestion holds

Textmetadata
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.