Evidence map›Paper›PMID 42289046›Full record

ArticleBriefings in bioinformatics2026

Reply to "Letter to the editor: methodological considerations in the benchmarking of AI-based protein-aptamer complex prediction".

Jiani Zhao, Kha Tram, Hongbin Yan, Yifeng Li

Abstract readLetter
PubMed Full text at PMC Publisher
In one paragraph

Article in Briefings in bioinformatics, 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

4 authors.

Jiani ZhaoDepartment of Computer Science, Brock University, 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario, Canada.
Kha TramCytodiagnostics Inc., 919 Fraser Dr Unit 11, Burlington L7L 4X8, Ontario, Canada.
Hongbin YanDepartment of Chemistry, Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario, Canada.
Yifeng LiDepartment of Computer Science, Brock University, 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario, Canada.ORCID 0000-0002-4873-6928

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We thank MD Kazim Okan Dolu for their interest in our published work and for the opportunity to clarify several points regarding software versioning, benchmark independence, secondary-structure generation, binding-free-energy terminology, and negative-control design. We acknowledge that several descriptions in the original manuscript could be stated more precisely. These clarifications improve the transparency and reproducibility of the study, but do not affect the reported analyses or main conclusions.

Indexed as

Aptamers, NucleotideArtificial IntelligenceProteinsBenchmarkingProtein BindingSoftwareAptamers, NucleotideProteinsbenchmarkingbinding free energyBoltz-2 versionDNA secondary structureindependent benchmarknegative control strategy

Identifiers

PMID42289046
PMCPMC13264833

What OpenQuestion holds

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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.