Evidence map›Paper›PMID 39850516›Full record

ArticleNature reviews bioengineering2024

Machine learning for antimicrobial peptide identification and design.

Fangping Wan, Felix Wong, James J Collins, Cesar de la Fuente-Nunez

Abstract read
In one paragraph

Article in Nature reviews bioengineering, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.

0numbers the graph read from it
0cells of the map it votes in
113citing 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

113 citing papers in PubMed.

  1. Artificial intelligence catalyzes antimicrobial peptide design.Synthetic and systems biotechnology · 2027
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53 more citing papers are in PubMed but not listed here.

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

4 authors.

Fangping WanMachine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Felix WongInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
James J CollinsInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-5560-8246
Cesar de la Fuente-NunezMachine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0002-2005-5629

Funding

Genetic, Metabolic and Regulatory Control of MIC and Relapse in M. tuberculosisR01AI146194 · NIAID · UNIVERSITY OF WASHINGTON · PI ALLAND, DAVID, SHERMAN, DAVID R · 2020 to 2024
$4.1M
Combining chemical and computational tools for predictive models of microbiome communitiesR35GM138201 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI DE LA FUENTE, CESAR · 2020 to 2024
$1.8M
Physical Biology and Deep Learning for Antibiotic Resistance and DiscoveryK25AI168451 · NIAID · BROAD INSTITUTE, INC. · PI Felix Wong · 2023 to 2026
$486k
NIAID NIH HHS K25 AI168451NIAID NIH HHS R01 AI146194NIGMS NIH HHS R35 GM138201
6 · The paper itself

Abstract

Artificial intelligence (AI) and machine learning (ML) models are being deployed in many domains of society and have recently reached the field of drug discovery. Given the increasing prevalence of antimicrobial resistance, as well as the challenges intrinsic to antibiotic development, there is an urgent need to accelerate the design of new antimicrobial therapies. Antimicrobial peptides (AMPs) are therapeutic agents for treating bacterial infections, but their translation into the clinic has been slow owing to toxicity, poor stability, limited cellular penetration and high cost, among other issues. Recent advances in AI and ML have led to breakthroughs in our abilities to predict biomolecular properties and structures and to generate new molecules. The ML-based modelling of peptides may overcome some of the disadvantages associated with traditional drug discovery and aid the rapid development and translation of AMPs. Here, we provide an introduction to this emerging field and survey ML approaches that can be used to address issues currently hindering AMP development. We also outline important limitations that can be addressed for the broader adoption of AMPs in clinical practice, as well as new opportunities in data-driven peptide design.

Identifiers

PMID39850516
PMCPMC11756916

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Registered trials

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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.