AlphaFold2
AlphaFold2, scored on ProteinBench; its model version and settings are not identified.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
14 evaluations · 14 results. Different protocols are not a single leaderboard.
Dataset subset: CAMEO2022, 183 proteins (ProteinBench split)
Sorted by GDT ts (mean over targets) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | GDT ts (mean over targets) | GDT ts (median over targets) | lDDT (mean over targets) | lDDT (median over targets) | Proteinbench ca break (mean over targets) | Proteinbench ca break (median over targets) | Proteinbench ca clash (mean over targets) | Proteinbench ca clash (median over targets) | Proteinbench pepbond break (mean over targets) | Proteinbench pepbond break (median over targets) | RMSD (mean over targets) | RMSD (median over targets) | TM score (mean over targets) | TM score (median over targets) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-GDT-TS-MEAN: Accuracy GDT-TS (mean) | 0.86 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-GDT-TS-MEDIAN: Accuracy GDT-TS (median) | Not reported | 0.921 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-LDDT-MEAN: Accuracy lDDT (mean) | Not reported | Not reported | 0.904 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-LDDT-MEDIAN: Accuracy lDDT (median) | Not reported | Not reported | Not reported | 0.933 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-RMSD-MEAN: Accuracy RMSD (mean) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 3.21 | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-RMSD-MEDIAN: Accuracy RMSD (median) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 1.64 | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-TM-SCORE-MEAN: Accuracy TM-score (mean) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.871 | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-ACCURACY-TM-SCORE-MEDIAN: Accuracy TM-score (median) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.952 |
| AlphaFold2Evaluation | ProteinBench FOLD-QUALITY-CA-BREAK-MEAN: Quality CA break (%) (mean) | Not reported | Not reported | Not reported | Not reported | 0% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-QUALITY-CA-BREAK-MEDIAN: Quality CA break (%) (median) | Not reported | Not reported | Not reported | Not reported | Not reported | 0% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-QUALITY-CA-CLASH-MEAN: Quality CA clash (%) (mean) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.3% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-QUALITY-CA-CLASH-MEDIAN: Quality CA clash (%) (median) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEAN: Quality PepBond break (%) (mean) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 4.8% | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaFold2Evaluation | ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEDIAN: Quality PepBond break (%) (median) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 4.1% | Not reported | Not reported | Not reported | Not reported |
All 14 result rows with coverage, uncertainty and sources
Filter evaluations
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-GDT-TS-MEAN: Accuracy GDT-TS (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.86 GDT ts (mean over targets) fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-GDT-TS-MEAN: Accuracy GDT-TS (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy GDT-TS ↑) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-GDT-TS-MEDIAN: Accuracy GDT-TS (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.921 GDT ts (median over targets) fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-GDT-TS-MEDIAN: Accuracy GDT-TS (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy GDT-TS ↑) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-LDDT-MEAN: Accuracy lDDT (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.904 lDDT (mean over targets) fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-LDDT-MEAN: Accuracy lDDT (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy lDDT ↑) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-LDDT-MEDIAN: Accuracy lDDT (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.933 lDDT (median over targets) fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-LDDT-MEDIAN: Accuracy lDDT (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy lDDT ↑) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-RMSD-MEAN: Accuracy RMSD (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 3.21 RMSD (mean over targets) unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-RMSD-MEAN: Accuracy RMSD (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy RMSD ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-RMSD-MEDIAN: Accuracy RMSD (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 1.64 RMSD (median over targets) unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-RMSD-MEDIAN: Accuracy RMSD (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy RMSD ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-TM-SCORE-MEAN: Accuracy TM-score (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.871 TM score (mean over targets) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-TM-SCORE-MEAN: Accuracy TM-score (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy TM-score ↑) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-ACCURACY-TM-SCORE-MEDIAN: Accuracy TM-score (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.952 TM score (median over targets) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-ACCURACY-TM-SCORE-MEDIAN: Accuracy TM-score (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Accuracy TM-score ↑) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-QUALITY-CA-BREAK-MEAN: Quality CA break (%) (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0% Proteinbench ca break (mean over targets) percent · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-QUALITY-CA-BREAK-MEAN: Quality CA break (%) (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Quality CA break (%) ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-QUALITY-CA-BREAK-MEDIAN: Quality CA break (%) (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0% Proteinbench ca break (median over targets) percent · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-QUALITY-CA-BREAK-MEDIAN: Quality CA break (%) (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Quality CA break (%) ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-QUALITY-CA-CLASH-MEAN: Quality CA clash (%) (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0.3% Proteinbench ca clash (mean over targets) percent · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-QUALITY-CA-CLASH-MEAN: Quality CA clash (%) (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Quality CA clash (%) ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-QUALITY-CA-CLASH-MEDIAN: Quality CA clash (%) (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 0% Proteinbench ca clash (median over targets) percent · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-QUALITY-CA-CLASH-MEDIAN: Quality CA clash (%) (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Quality CA clash (%) ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEAN: Quality PepBond break (%) (mean) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 4.8% Proteinbench pepbond break (mean over targets) percent · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEAN: Quality PepBond break (%) (mean) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Quality PepBond break (%) ↓) |
| Configuration: AlphaFold2 | Task: ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEDIAN: Quality PepBond break (%) (median) Dataset subset: CAMEO2022, 183 proteins (ProteinBench split) | 4.1% Proteinbench pepbond break (median over targets) percent · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAlphaFold2 on ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEDIAN: Quality PepBond break (%) (median) Structure prediction on CAMEO2022. Each cell prints the mean and the median over 183 proteins. Aggregation: Not reported proteinbench primary benchmark evidence · Table 7, row(AlphaFold2), column(Quality PepBond break (%) ↓) |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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How it works, versions and access
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Evidence
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Evidence table
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- proteinbench primary benchmark evidence · Original source · 2409.06744v1
Technical metadata and extraction receipts
Stable ID: proteinbench-method-alphafold2
- areas
- proteins-complexes
- source locator
- Table 7, row(AlphaFold2)
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
- provenance note
- Protein model evaluated by the ProteinBench authors under their harness.
Related records
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-GDT-TS-MEAN: Accuracy GDT-TS (mean)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-GDT-TS-MEDIAN: Accuracy GDT-TS (median)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-LDDT-MEAN: Accuracy lDDT (mean)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-LDDT-MEDIAN: Accuracy lDDT (median)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-RMSD-MEAN: Accuracy RMSD (mean)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-RMSD-MEDIAN: Accuracy RMSD (median)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-TM-SCORE-MEAN: Accuracy TM-score (mean)
- system: AlphaFold2 on ProteinBench FOLD-ACCURACY-TM-SCORE-MEDIAN: Accuracy TM-score (median)
- system: AlphaFold2 on ProteinBench FOLD-QUALITY-CA-BREAK-MEAN: Quality CA break (%) (mean)
- system: AlphaFold2 on ProteinBench FOLD-QUALITY-CA-BREAK-MEDIAN: Quality CA break (%) (median)
- system: AlphaFold2 on ProteinBench FOLD-QUALITY-CA-CLASH-MEAN: Quality CA clash (%) (mean)
- system: AlphaFold2 on ProteinBench FOLD-QUALITY-CA-CLASH-MEDIAN: Quality CA clash (%) (median)
- system: AlphaFold2 on ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEAN: Quality PepBond break (%) (mean)
- system: AlphaFold2 on ProteinBench FOLD-QUALITY-PEPBOND-BREAK-MEDIAN: Quality PepBond break (%) (median)