Evidence map›Paper›PMID 36399057›Full record

ArticleGigaScience2022

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals.

Yunchi Zhu, Xin Liao, Tingyu Han, J-Y Chen, Chunpeng He, Zuhong Lu

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.7field-weighted citation impact, top 28% 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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. MineProt: a stand-alone server for structural proteome curation.Database : the journal of biological databases and curation · 2023
    Article
  2. 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 at 3 institutions in 1 country.

Yunchi ZhuState Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, 210096, China.ORCID 0000-0003-0818-2585
Xin LiaoGuangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai 536000, China.
Tingyu HanState Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, 210096, China.
J-Y ChenNanjing Institute of Paleontology and Geology, Chinese Academy of Sciences, Nanjing 210008, China.
Chunpeng HeState Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, 210096, China.ORCID 0000-0003-0566-5397
Zuhong LuState Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, 210096, China.
Southeast University · CNChinese Academy of Sciences · CNGuangxi Mangrove Research Center · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundReef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals.

resultsOf the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence.

conclusionsOur work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

Indexed as

AnthozoaAnimalsArtificial IntelligenceCoral ReefsEcosystemProteomeReproducibility of ResultsProteomeColabFoldreef-building coralstructural proteomics

Identifiers

PMID36399057
PMCPMC9673494
OpenAlexW4309665402

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.