Evidence map›Paper›PMID 41866819›Full record

ArticleJournal of chemical information and modeling2026

Physical Implausibility of Carbohydrate Ligands in Results of Deep Learning-Based Cofolding Methods.

Muhammad Luthfi, Adam J Simpkin, Luc G Elliott, Pornthep Sompornpisut, Daniel J Rigden

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of chemical information and modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

5 authors.

Muhammad LuthfiProgram in Bioinformatics and Computational Biology, College of Interdisciplinary and Integrative Studies, Chulalongkorn University, Bangkok 10330, Thailand.
Adam J SimpkinDepartment of Biochemistry, Cell and Systems Biology; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
Luc G ElliottDepartment of Biochemistry, Cell and Systems Biology; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
Pornthep SompornpisutCenter of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok 10330, Thailand.ORCID 0000-0002-8029-332X
Daniel J RigdenDepartment of Biochemistry, Cell and Systems Biology; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.ORCID 0000-0002-7565-8937

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Stereochemistry violations in AlphaFold 3 models are more prevalent than currently appreciated. Analysis of 900 carbohydrate ligands revealed that 85.8% have errors, mainly in chirality but also including bond conversions (15.2%), planar ring distortions (3.9%), aromatic ring formations (2.5%), and improper structural configurations (0.9%). Boltz-1x reduced most violations dramatically but increased improper configurations to 22.1%, notably in

Indexed as

CarbohydratesDeep LearningCarbohydrate ConformationLigandsModels, MolecularStereoisomerismCarbohydratesLigands

Identifiers

PMID41866819
PMCPMC13080964

What OpenQuestion holds

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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.