Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is electron microscopy (Table 2, column 'EM') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 37 Count (Acceptable quality (0.23 <= DockQ < 0.49); structures in the class whose experimental reference is electron microscopy)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 dimeric predictive-class counts, structures in the class whose experimental reference is electron microscopy (Table 2)
lit-structure-20261011-afesmfold-protocol-2-em
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'EM' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is electron microscopy (Table 2, column 'EM') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 43 Count (High quality (DockQ >= 0.80); structures in the class whose experimental reference is electron microscopy)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 dimeric predictive-class counts, structures in the class whose experimental reference is electron microscopy (Table 2)
lit-structure-20261011-afesmfold-protocol-2-em
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'High quality', column 'EM' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is electron microscopy (Table 2, column 'EM') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 47 Count (Incorrect prediction (DockQ < 0.23); structures in the class whose experimental reference is electron microscopy)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 dimeric predictive-class counts, structures in the class whose experimental reference is electron microscopy (Table 2)
lit-structure-20261011-afesmfold-protocol-2-em
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Incorrect prediction', column 'EM' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is electron microscopy (Table 2, column 'EM') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 91 Count (Medium quality (0.49 <= DockQ < 0.80); structures in the class whose experimental reference is electron microscopy)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 dimeric predictive-class counts, structures in the class whose experimental reference is electron microscopy (Table 2)
lit-structure-20261011-afesmfold-protocol-2-em
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Medium quality', column 'EM' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, heterodimeric structures in the class (Table 2, column 'Heterodimer') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 21 Count (Acceptable quality (0.23 <= DockQ < 0.49); heterodimeric structures in the class)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 dimeric predictive-class counts, heterodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-heterodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'Heterodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, heterodimeric structures in the class (Table 2, column 'Heterodimer') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 74 Count (High quality (DockQ >= 0.80); heterodimeric structures in the class)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 dimeric predictive-class counts, heterodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-heterodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'High quality', column 'Heterodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, heterodimeric structures in the class (Table 2, column 'Heterodimer') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 31 Count (Incorrect prediction (DockQ < 0.23); heterodimeric structures in the class)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 dimeric predictive-class counts, heterodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-heterodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Incorrect prediction', column 'Heterodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, heterodimeric structures in the class (Table 2, column 'Heterodimer') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 73 Count (Medium quality (0.49 <= DockQ < 0.80); heterodimeric structures in the class)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 dimeric predictive-class counts, heterodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-heterodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Medium quality', column 'Heterodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) 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) 84 Count (Acceptable quality (0.23 <= DockQ < 0.49); homodimeric structures in the class)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 dimeric predictive-class counts, homodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-homodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'Homodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) 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) 287 Count (High quality (DockQ >= 0.80); homodimeric structures in the class)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 dimeric predictive-class counts, homodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-homodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'High quality', column 'Homodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) 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) 200 Count (Incorrect prediction (DockQ < 0.23); homodimeric structures in the class)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 dimeric predictive-class counts, homodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-homodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Incorrect prediction', column 'Homodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) 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) 224 Count (Medium quality (0.49 <= DockQ < 0.80); homodimeric structures in the class)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 dimeric predictive-class counts, homodimeric structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-homodimer
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Medium quality', column 'Homodimer' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is NMR (Table 2, column 'NMR') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 5 Count (Acceptable quality (0.23 <= DockQ < 0.49); structures in the class whose experimental reference is NMR)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 dimeric predictive-class counts, structures in the class whose experimental reference is NMR (Table 2)
lit-structure-20261011-afesmfold-protocol-2-nmr
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'NMR' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is NMR (Table 2, column 'NMR') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 0 Count (High quality (DockQ >= 0.80); structures in the class whose experimental reference is NMR)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 dimeric predictive-class counts, structures in the class whose experimental reference is NMR (Table 2)
lit-structure-20261011-afesmfold-protocol-2-nmr
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'High quality', column 'NMR' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is NMR (Table 2, column 'NMR') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 3 Count (Incorrect prediction (DockQ < 0.23); structures in the class whose experimental reference is NMR)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 dimeric predictive-class counts, structures in the class whose experimental reference is NMR (Table 2)
lit-structure-20261011-afesmfold-protocol-2-nmr
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Incorrect prediction', column 'NMR' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose experimental reference is NMR (Table 2, column 'NMR') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 7 Count (Medium quality (0.49 <= DockQ < 0.80); structures in the class whose experimental reference is NMR)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 dimeric predictive-class counts, structures in the class whose experimental reference is NMR (Table 2)
lit-structure-20261011-afesmfold-protocol-2-nmr
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Medium quality', column 'NMR' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, all structures in the class (Table 2, column 'No.') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 105 Count (Acceptable quality (0.23 <= DockQ < 0.49); all structures in the class)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 dimeric predictive-class counts, all structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-no
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'No.' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, all structures in the class (Table 2, column 'No.') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 361 Count (High quality (DockQ >= 0.80); all structures in the class)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 dimeric predictive-class counts, all structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-no
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'High quality', column 'No.' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, all structures in the class (Table 2, column 'No.') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 231 Count (Incorrect prediction (DockQ < 0.23); all structures in the class)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 dimeric predictive-class counts, all structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-no
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Incorrect prediction', column 'No.' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, all structures in the class (Table 2, column 'No.') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 297 Count (Medium quality (0.49 <= DockQ < 0.80); all structures in the class)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 dimeric predictive-class counts, all structures in the class (Table 2)
lit-structure-20261011-afesmfold-protocol-2-no
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Medium quality', column 'No.' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose pLDDT is at least 70 (Table 2, column 'pLDDT ≥ 70') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 92 Count (Acceptable quality (0.23 <= DockQ < 0.49); structures in the class whose pLDDT is at least 70)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 dimeric predictive-class counts, structures in the class whose pLDDT is at least 70 (Table 2)
lit-structure-20261011-afesmfold-protocol-2-plddt-ge-70
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'pLDDT ≥ 70' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose pLDDT is at least 70 (Table 2, column 'pLDDT ≥ 70') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 356 Count (High quality (DockQ >= 0.80); structures in the class whose pLDDT is at least 70)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 dimeric predictive-class counts, structures in the class whose pLDDT is at least 70 (Table 2)
lit-structure-20261011-afesmfold-protocol-2-plddt-ge-70
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'High quality', column 'pLDDT ≥ 70' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose pLDDT is at least 70 (Table 2, column 'pLDDT ≥ 70') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 197 Count (Incorrect prediction (DockQ < 0.23); structures in the class whose pLDDT is at least 70)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 dimeric predictive-class counts, structures in the class whose pLDDT is at least 70 (Table 2)
lit-structure-20261011-afesmfold-protocol-2-plddt-ge-70
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Incorrect prediction', column 'pLDDT ≥ 70' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class whose pLDDT is at least 70 (Table 2, column 'pLDDT ≥ 70') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 283 Count (Medium quality (0.49 <= DockQ < 0.80); structures in the class whose pLDDT is at least 70)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 dimeric predictive-class counts, structures in the class whose pLDDT is at least 70 (Table 2)
lit-structure-20261011-afesmfold-protocol-2-plddt-ge-70
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Medium quality', column 'pLDDT ≥ 70' Configuration: AlphaFold2 (AlphaFold2 v2.2.3 installed locally; five models per sequence) Protocol: Predictive-class counts for dimeric predictions, structures in the class with template quality 0 (no homologous pre-2022 structure) (Table 2, column 'TQ 0') Dataset: 994 non-redundant dimeric PDB structures (2022-2024) 59 Count (Acceptable quality (0.23 <= DockQ < 0.49); structures in the class with template quality 0 (no homologous pre-2022 structure))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 dimeric predictive-class counts, structures in the class with template quality 0 (no homologous pre-2022 structure) (Table 2)
lit-structure-20261011-afesmfold-protocol-2-tq-0
Aggregation: Not reported
Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins · Table 2, row 'AlphaFold2' / 'Acceptable quality', column 'TQ 0'