Evidence map›Paper›PMID 40792509›Full record

ArticleMicrobiology spectrum2025

AlphaFold 3 accurately models natural variants of

Andrea Gomez, Arden Baylink

Abstract read
In one paragraph

Article in Microbiology spectrum, 2025. 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
–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

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

2 authors.

Andrea GomezDepartment of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA.ORCID 0000-0002-1677-732X
Arden BaylinkDepartment of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA.ORCID 0000-0001-5522-769X

Funding

Understanding the molecular mechanisms and biological functions of a novel bleach-sensing bacterial receptor in shaping host-associated bacterial populations in response to host inflammationR00AI148587 · NIAID · WASHINGTON STATE UNIVERSITY · PI BAYLINK, ARDEN · 2022 to 2023
$498k
Understanding the molecular mechanisms and biological functions of a novel bleach-sensing bacterial receptor in shaping host-associated bacterial populations in response to host inflammationK99AI148587 · NIAID · UNIVERSITY OF OREGON · PI BAYLINK, ARDEN · 2020 to 2021
$235k
National Institute of Allergy and Infectious Diseases 1K99AI148587, 4R00AI148587-03NIAID NIH HHS K99 AI148587NIAID NIH HHS R00 AI148587
6 · The paper itself

Abstract

Subtle changes in protein sequence can equate to large changes in function, such as enabling pathogens to evade the immune system, hindering antibody recognition of antigens, or conferring antibiotic resistance. Even single amino acid substitutions may alter ligand binding affinity, enzymatic activity, and protein stability. Yet, due to limitations in time and resources, proteins closely related in sequence to those already characterized often remain unexamined. AlphaFold has emerged as a promising tool for protein structure prediction, though its utility in modeling single amino acid substitutions remains uncertain. In this study, we assessed AlphaFold 3's accuracy in modeling natural variants of the

Indexed as

Bacterial ProteinsCatalaseHelicobacter pyloriAmino Acid SequenceAmino Acid SubstitutionModels, MolecularProtein ConformationBacterial ProteinsCatalaseAlphaFoldcatalaseHelicobacternatural variants

Identifiers

PMID40792509
PMCPMC12403698

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.