Result

Count (Incorrect prediction (DockQ < 0.23); homodimeric structures in the class) of AlphaFold3 (AlphaFold3 accessed as a web service) on 994 non-redundant dimeric PDB structures (2022-2024)

219 Count (Incorrect prediction (DockQ < 0.23); homodimeric structures in the class)

Evidence concern: excluded from comparisons

The ESMFold rows give 244 EM and 107 NMR monomers, while the AlphaFold2 and AlphaFold3 rows over the same 1666 targets give 161 and 190, and the text gives 160 and 190. The Discussion says ESMFold mispredicted 139 of 190 NMR monomers, against 56 incorrect and 9 special cases in the table. The EM and NMR cells of the ESMFold incorrect row appear transposed.Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, ESMFold rows, columns 'EM' and 'NMR'; Results paragraph 17; Discussion

The text says all 11 AlphaFold2 and all 11 AlphaFold3 special cases are NMR structures; the table gives 1 XRD and 10 NMR for AlphaFold2, and 2 XRD, 1 EM and 8 NMR for AlphaFold3.Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, 'Special cases' rows, columns 'XRD', 'EM', 'NMR'; Results paragraphs 24 and 27

The row prints EM 3 and NMR 37, so AlphaFold3 totals 184 EM and 49 NMR against 218 and 15 for the other tools over the same 994 targets (text: 219 and 15). The two cells appear transposed.Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, AlphaFold3 'Acceptable quality' row, columns 'EM' and 'NMR'

Template quality is a property of the target, yet the column totals differ by tool (TQ 0: 557, 319 and 391). For AlphaFold3 the text gives 414, 326 and 5 accurate and 153, 88 and 8 incorrect dimers by TQ band, against 228, 512 and 4, and 91, 158 and 0, in the table.Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, columns 'TQ 0', 'TQ 1–40', 'TQ > 40'; Results paragraph 38

Several rows do not sum to the 'No.' column: Table 1 AlphaFold2 and AlphaFold3 accurate (method columns 1068 and 1075), ESMFold domain movement (429); Table 2 AlphaFold2 incorrect (method 230), AlphaFold3 medium (TQ 305), ESMFold acceptable (TQ 122) and incorrect (method and TQ 584).Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Tables 1 and 2, row totals

Methods

Tested configuration: AlphaFold3 (AlphaFold3 accessed as a web service)
Protocol: Predictive-class counts for dimeric predictions, homodimeric structures in the class (Table 2, column 'Homodimer')
Dataset: 994 non-redundant dimeric PDB structures (2022-2024)
Procedure: Predictive-class counts for dimeric predictions, homodimeric structures in the class (Table 2, column 'Homodimer')
Evaluation: AlphaFold3 dimeric predictive-class counts, homodimeric structures in the class (Table 2)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedComparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold3' / 'Incorrect prediction', column 'Homodimer'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: PDB dimeric structures released 2022-2024 without close pre-2022 homologues
Adaptation: None; tools run as released
Scoring implementation: Counts of predicted structures per predictive class

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Reported result 219 Individual claims	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, row 'AlphaFold3' / 'Incorrect prediction', column 'Homodimer' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Extraction: Parsed the pinned Europe PMC JATS XML with extract_afesmfold.py (table-wrap grid with rowspan and colspan expanded, tool column forward-filled); row and column labels asserted. Table 2, row 'AlphaFold3' / 'Incorrect prediction', column 'Homodimer' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md. Field: `attributes.printed_value` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Extraction artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Original source · Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text)

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Technical metadata and extraction receipts

Stable ID: lit-structure-20261011-afesmfold-result-2-alphafold3-homodimer-incorrect-prediction

metric: count
metric direction: unknown
unit: count
printed value: 219
source locator: Table 2, row 'AlphaFold3' / 'Incorrect prediction', column 'Homodimer'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Reviewer re-retrieved the Europe PMC JATS XML and matched its SHA-256; an independent table-grid parse matched all 216 results; a hand sample of 48 values against the rendered PMC HTML matched; row and column totals cross-checked against the text.; reviewer: claude; reviewer note: Claude review agent reviewer-ps-2, independent of the extractor lit-protein-structure; no human review claimed; date: 2026-10-11; artifact sha256: aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12809598/fullTextXML; note: Extraction: Parsed the pinned Europe PMC JATS XML with extract_afesmfold.py (table-wrap grid with rowspan and colspan expanded, tool column forward-filled); row and column labels asserted. Table 2, row 'AlphaFold3' / 'Incorrect prediction', column 'Homodimer' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md.
numeric value: 219
metric qualifier: Incorrect prediction (DockQ < 0.23); homodimeric structures in the class
unit detail: predicted structures
missing metadata: uncertainty: reason: unreported
score category: Incorrect prediction
printed value basis: Integer count as printed

Related records

evaluation: AlphaFold3 dimeric predictive-class counts, homodimeric structures in the class (Table 2)

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