Protocol

Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD')

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

Monomer predictions were compared with the experimental structure by RMSD and LDDT and assigned to one of four predictive classes: accurate prediction (RMSD <= 3.0 Angstrom and LDDT >= 0.7), correct with domain movement (RMSD > 3.0 Angstrom and LDDT >= 0.7), incorrect prediction (RMSD > 3.0 Angstrom and LDDT < 0.7) and special cases (LDDT < 0.7 and RMSD < 3.0 Angstrom). This protocol counts, for each class, structures in the class whose experimental reference is X-ray diffraction.

3 evaluations · 12 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

3 recorded evaluations, 12 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

3 evaluations · 12 results. Different protocols are not a single leaderboard.

Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') · Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)

In source order. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Count (Accurate prediction (RMSD <= 3.0 Angstrom and LDDT >= 0.7); structures in the class whose experimental reference is X-ray diffraction)	Count (Domain movement (RMSD > 3.0 Angstrom and LDDT >= 0.7 (correct folds, different domain arrangement)); structures in the class whose experimental reference is X-ray diffraction)	Count (Incorrect prediction (RMSD > 3.0 Angstrom and LDDT < 0.7); structures in the class whose experimental reference is X-ray diffraction)	Count (Special cases (LDDT < 0.7 and RMSD < 3.0 Angstrom); structures in the class whose experimental reference is X-ray diffraction)
AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence)Evaluation	985	281	47	1
AlphaFold3 (AlphaFold3 accessed as a web service)Evaluation	1001	274	37	2
ESMFold (ESMFold installed locally from its GitHub repository)Evaluation	783	332	195	4

All 12 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	985 Count (Accurate prediction (RMSD <= 3.0 Angstrom and LDDT >= 0.7); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold2 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold2' / 'Accurate prediction', column 'XRD'
Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	281 Count (Domain movement (RMSD > 3.0 Angstrom and LDDT >= 0.7 (correct folds, different domain arrangement)); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold2 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold2' / 'Domain movement', column 'XRD'
Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	47 Count (Incorrect prediction (RMSD > 3.0 Angstrom and LDDT < 0.7); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold2 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold2' / 'Incorrect prediction', column 'XRD'
Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	1 Count (Special cases (LDDT < 0.7 and RMSD < 3.0 Angstrom); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold2 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold2' / 'Special cases', column 'XRD'
Configuration: AlphaFold3 (AlphaFold3 accessed as a web service)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	1000 Count (Accurate prediction (RMSD <= 3.0 Angstrom and LDDT >= 0.7); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold3 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold3' / 'Accurate prediction', column 'XRD'
Configuration: AlphaFold3 (AlphaFold3 accessed as a web service)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	274 Count (Domain movement (RMSD > 3.0 Angstrom and LDDT >= 0.7 (correct folds, different domain arrangement)); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold3 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold3' / 'Domain movement', column 'XRD'
Configuration: AlphaFold3 (AlphaFold3 accessed as a web service)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	37 Count (Incorrect prediction (RMSD > 3.0 Angstrom and LDDT < 0.7); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold3 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold3' / 'Incorrect prediction', column 'XRD'
Configuration: AlphaFold3 (AlphaFold3 accessed as a web service)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	2 Count (Special cases (LDDT < 0.7 and RMSD < 3.0 Angstrom); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source AlphaFold3 monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'AlphaFold3' / 'Special cases', column 'XRD'
Configuration: ESMFold (ESMFold installed locally from its GitHub repository)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	783 Count (Accurate prediction (RMSD <= 3.0 Angstrom and LDDT >= 0.7); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source ESMFold monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'ESMFold' / 'Accurate prediction', column 'XRD'
Configuration: ESMFold (ESMFold installed locally from its GitHub repository)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	332 Count (Domain movement (RMSD > 3.0 Angstrom and LDDT >= 0.7 (correct folds, different domain arrangement)); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source ESMFold monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'ESMFold' / 'Domain movement', column 'XRD'
Configuration: ESMFold (ESMFold installed locally from its GitHub repository)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	195 Count (Incorrect prediction (RMSD > 3.0 Angstrom and LDDT < 0.7); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source ESMFold monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'ESMFold' / 'Incorrect prediction', column 'XRD'
Configuration: ESMFold (ESMFold installed locally from its GitHub repository)	Protocol: Predictive-class counts for monomeric predictions, structures in the class whose experimental reference is X-ray diffraction (Table 1, column 'XRD') Dataset: 1666 non-redundant monomeric PDB structures (2022-2024)	4 Count (Special cases (LDDT < 0.7 and RMSD < 3.0 Angstrom); structures in the class whose experimental reference is X-ray diffraction) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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, coverage and source ESMFold monomeric predictive-class counts, structures in the class whose experimental reference is X-ray diffraction (Table 1) lit-structure-20261011-afesmfold-protocol-1-xrd Aggregation: Not reported Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 1, row 'ESMFold' / 'Special cases', column 'XRD'

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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: lit-structure-20261011-afesmfold-protocol-1-xrd

areas: protein-structure; proteins-complexes
contexts: research
protocol: Monomer predictions were compared with the experimental structure by RMSD and LDDT and assigned to one of four predictive classes: accurate prediction (RMSD <= 3.0 Angstrom and LDDT >= 0.7), correct with domain movement (RMSD > 3.0 Angstrom and LDDT >= 0.7), incorrect prediction (RMSD > 3.0 Angstrom and LDDT < 0.7) and special cases (LDDT < 0.7 and RMSD < 3.0 Angstrom).
metric: count
metric direction: unknown
unit: count
unit detail: predicted structures
metric qualifier: structures in the class whose experimental reference is X-ray diffraction
version: As published 2026
source locator: Table 1, column 'XRD'; Materials and methods (classification thresholds)
limitations: Counts per class, not a single accuracy score.; Template quality is defined in the text as sequence identity multiplied by query coverage.

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