Evidence map›Paper›PMID 38531599›Full record

ArticleDatabase : the journal of biological databases and curation2024

ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides.

Hongfang Wu, Rongxian Chen, Xuejian Li, Yue Zhang, Jianwei Zhang, Yanbo Yang, Jun Wan, Yang Zhou, Huanchun Chen, Jinquan Li and 2 more

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

Article in Database : the journal of biological databases and curation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
6.0field-weighted citation impact, top 4% 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

6 citing papers in PubMed, 13 citations in OpenAlex.

  1. Antibiofilm efficacy of phage W5 against antimicrobial-resistantApplied and environmental microbiology · 2026
    Article
  2. Review
  3. Article
  4. Review
  5. Article
  6. Antimicrobial resistance inScience in One Health · 2025
    Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors at 1 institution in 1 country.

Hongfang WuNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Rongxian ChenNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Xuejian LiNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Yue ZhangNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Jianwei ZhangNational Key Laboratory of Crop Genetic Improvement, Shizishan Street No. 1, Wuhan 430070, China.ORCID 0000-0001-8030-5346
Yanbo YangCollege of Informatics, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Jun WanHubei Hongshan Laboratory, College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Yang ZhouCollege of Fisheries, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Huanchun ChenNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Jinquan LiNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Runze LiNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Geng ZouNational Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Huazhong Agricultural University · CN

Funding

HZAU-AGIS Cooperation Fund SZYJY2022027National Natural Science Foundation of China 32072323, 32073022, 31772083Natural Science Foundation of Hubei Province 2022CFB659
6 · The paper itself

Abstract

'Superbugs' have received increasing attention from researchers, such as ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.), which directly led to about 1 270 000 death cases in 2019. Recently, phage peptidoglycan hydrolases (PGHs)-derived antimicrobial peptides were proposed as new antibacterial agents against multidrug-resistant bacteria. However, there is still a lack of methods for mining antimicrobial peptides based on phages or phage PGHs. Here, by using a collection of 6809 genomes of ESKAPE isolates and corresponding phages in public databases, based on a unified annotation process of all the genomes, PGHs were systematically identified, from which peptides were mined. As a result, a total of 12 067 248 peptides with high antibacterial activities were respectively determined. A user-friendly tool was developed to predict the phage PGHs-derived antimicrobial peptides from customized genomes, which also allows the calculation of peptide phylogeny, physicochemical properties, and secondary structure. Finally, a user-friendly and intuitive database, ESKtides (http://www.phageonehealth.cn:9000/ESKtides), was designed for data browsing, searching and downloading, which provides a rich peptide library based on ESKAPE prophages and phages. Database URL:  10.1093/database/baae022.

Indexed as

Antimicrobial PeptidesBacteriophagesAnti-Bacterial AgentsBacteriaKlebsiella pneumoniaeAnti-Bacterial AgentsAntimicrobial Peptides

Identifiers

PMID38531599
PMCPMC10965241
OpenAlexW4393184503

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.