Evidence claim

Relevance of dimeric predictive-class counts to "Choose structural hypotheses to guide experiments"

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

Use case: Choose structural hypotheses to guide experiments
Assessed by: Predictive-class counts for dimeric predictions, all structures in the class (Table 2, column 'No.')
Relevance: Proxy evidence
Endpoint: Number of dimeric targets each tool places in each predictive class, out of 994 dimers

How often AlphaFold2, AlphaFold3 and ESMFold get dimeric structures right on targets released after their training data, as evidence for trusting a predicted structure.

3 reviewed evaluations

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.

17 evidence rows 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
Citation locations 1 values source id lit-structure-20261011-afesmfold-source-mahtha2026 locator Table 2, column 'No.' Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group protein-protein-interfaces Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Protein-protein interface predictions Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values Counts, not rates: divide by 1666 (monomers) or 994 (dimers) before comparing tools. The classification thresholds are the authors' own; compare only within this protocol. Inspect every linked evaluation's source locator before citing a result. Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.constraints` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Number of dimeric targets each tool places in each predictive class, out of 994 dimers Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.endpoint` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:lit-structure-20261011-afesmfold-protocol-2-no Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric count Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 6 values Automated transcription of the printed counts; no independent reproduction of the predictions or the classification. AlphaFold3 was run through its web service while AlphaFold2 and ESMFold were run locally, so compute settings differ between tools. The per-target lists are on the authors' portal and were not retrieved. The table's experimental-method and template-quality columns conflict with the text in places (see the source's evidence concerns); the linked 'No.' column agrees with the text. For dimers, the AlphaFold2 and AlphaFold3 model scored is the best of five by DockQ against the experimental structure (Methods paragraph 14), a selection a user cannot make; ESMFold gives one model, so the comparison favours AlphaFold. Dimers were kept when only one chain lacked a close pre-2022 homologue (Methods paragraph 6). Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.limitations` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale Proxy: the dimer classes are DockQ bands over homodimers and heterodimers together, so they bear on whether a predicted interface is worth testing but do not separate the antibody, peptide or ligand complex classes the use case treats separately. Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.rationale` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Reason Not shown: the source's experimental-method, template-quality and row-total cells conflict with its own text in places, recorded as evidence concerns on the source. This judgement uses only the 'No.' column, which agrees with the text, but a source with evidence concerns withholds every judgement that cites it until the concerns are resolved. Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Table 2, column 'No.' Version: Version of record, NAR Genomics and Bioinformatics 2026 (PMC12809598 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.reason` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: needs review

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: use-case-mapping-lit-structure-20261011-afesmfold-dimeric

field: links:assessed_by:lit-structure-20261011-afesmfold-protocol-2-no
value: lit-structure-20261011-afesmfold-protocol-2-no
relevance: proxy
endpoint: Number of dimeric targets each tool places in each predictive class, out of 994 dimers
rationale: Proxy: the dimer classes are DockQ bands over homodimers and heterodimers together, so they bear on whether a predicted interface is worth testing but do not separate the antibody, peptide or ligand complex classes the use case treats separately.
constraints: Counts, not rates: divide by 1666 (monomers) or 994 (dimers) before comparing tools.; The classification thresholds are the authors' own; compare only within this protocol.; Inspect every linked evaluation's source locator before citing a result.
limitations: Automated transcription of the printed counts; no independent reproduction of the predictions or the classification.; AlphaFold3 was run through its web service while AlphaFold2 and ESMFold were run locally, so compute settings differ between tools.; The per-target lists are on the authors' portal and were not retrieved.; The table's experimental-method and template-quality columns conflict with the text in places (see the source's evidence concerns); the linked 'No.' column agrees with the text.; For dimers, the AlphaFold2 and AlphaFold3 model scored is the best of five by DockQ against the experimental structure (Methods paragraph 14), a selection a user cannot make; ESMFold gives one model, so the comparison favours AlphaFold.; Dimers were kept when only one chain lacked a close pre-2022 homologue (Methods paragraph 6).
citation locators: source id: lit-structure-20261011-afesmfold-source-mahtha2026; locator: Table 2, column 'No.'
source locator: Table 2, column 'No.'
headline metric: count
comparison group: protein-protein-interfaces
comparison title: Protein-protein interface predictions
stratum label: DockQ classes on 994 post-2021 dimers (Mahtha et al. 2026)
reviewed evaluations: lit-structure-20261011-afesmfold-eval-2-alphafold2-no; lit-structure-20261011-afesmfold-eval-2-alphafold3-no; lit-structure-20261011-afesmfold-eval-2-esmfold-no
reason: Not shown: the source's experimental-method, template-quality and row-total cells conflict with its own text in places, recorded as evidence concerns on the source. This judgement uses only the 'No.' column, which agrees with the text, but a source with evidence concerns withholds every judgement that cites it until the concerns are resolved.

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subject: Choose structural hypotheses to guide experiments

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