Evidence claim

printed_value_conflict: lit-structure-20261011-afesmfold-source-mahtha2026

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

Printed value conflict of Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins

The Abstract prints ESMFold monomer accuracy as 76%: 'On the other hand, ESMFold accurately predicted 76% of the monomeric proteins and 41% of the dimeric proteins.' The Discussion prints 77%: 'For monomeric proteins, AlphaFold2 and AlphaFold3 exhibited comparable performance, each accurately predicting 87%–88% of the structures, while ESMFold achieved 77% accuracy.' Table 1 and the Results give ESMFold 832 accurate predictions (50%) and 430 with domain movement (26%) out of 1,666 monomers. The paper does not print the sum; 832 + 430 = 1,262 of 1,666 is 75.75% (computed here, not printed), which rounds to the Abstract's 76%, not to the Discussion's 77%.

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field printed_value_conflict Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', 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
Source location Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', column 'No.' Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', 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.source_locator` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value The Abstract prints ESMFold monomer accuracy as 76%: 'On the other hand, ESMFold accurately predicted 76% of the monomeric proteins and 41% of the dimeric proteins.' The Discussion prints 77%: 'For monomeric proteins, AlphaFold2 and AlphaFold3 exhibited comparable performance, each accurately predicting 87%–88% of the structures, while ESMFold achieved 77% accuracy.' Table 1 and the Results give ESMFold 832 accurate predictions (50%) and 430 with domain movement (26%) out of 1,666 monomers. The paper does not print the sum; 832 + 430 = 1,262 of 1,666 is 75.75% (computed here, not printed), which rounds to the Abstract's 76%, not to the Discussion's 77%. Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', 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.value` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Descriptive fact transcribed from the pinned source. Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', 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: `description` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: subject lit-structure-20261011-afesmfold-source-mahtha2026 Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', 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: `links:subject:lit-structure-20261011-afesmfold-source-mahtha2026` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name printed_value_conflict: lit-structure-20261011-afesmfold-source-mahtha2026 Context-only references	Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins Original source ↗ Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', 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: `name` Source artifact SHA-256: `aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

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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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Stable ID: gfm-guides-20261014-mahtha2026-claim-esmfold-monomer-accuracy-abstract-vs-discussion

field: printed_value_conflict
value: The Abstract prints ESMFold monomer accuracy as 76%: 'On the other hand, ESMFold accurately predicted 76% of the monomeric proteins and 41% of the dimeric proteins.' The Discussion prints 77%: 'For monomeric proteins, AlphaFold2 and AlphaFold3 exhibited comparable performance, each accurately predicting 87%–88% of the structures, while ESMFold achieved 77% accuracy.' Table 1 and the Results give ESMFold 832 accurate predictions (50%) and 430 with domain movement (26%) out of 1,666 monomers. The paper does not print the sum; 832 + 430 = 1,262 of 1,666 is 75.75% (computed here, not printed), which rounds to the Abstract's 76%, not to the Discussion's 77%.
source locator: Abstract sentence 4; Discussion paragraph 1, sentence 6; Results section 'Performance of ESMFold for monomer structure prediction' paragraph 1, sentence 1; Table 1, ESMFold rows 'Accurate prediction' and 'Domain movement', column 'No.'
review: method: source-hash-verification; transcription; method note: Europe PMC JATS re-downloaded on 2026-10-14 (SHA-256 matches the source record); Abstract, Discussion, Results and Table 1 re-read.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-14; artifact sha256: aae321d05839186a7595987d05af6e95aec5ac32b93b35c5cf1126902fe798b8; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12809598/fullTextXML; note: Extraction: Europe PMC JATS re-downloaded on 2026-10-14 (SHA-256 matches the source record); extract/build_claim.py asserts the Abstract, Discussion and Results sentences and the two Table 1 cells. Independent review 2026-10-14: matched. The Results define the AlphaFold2 figure the same way ('An additional 386 ... were also considered as correct predictions. Taken together, AlphaFold2 achieved 87.4% accuracy'), which supports reading 'accuracy' as accurate plus domain movement. No evidence concern added: the stored results are Table 1 counts, which agree with the Results text.

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subject: Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins

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