AbDPO
AbDPO, 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
13 evaluations · 13 results. Different protocols are not a single leaderboard.
Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)
Sorted by Proteinbench binding energy (lower 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 | Proteinbench binding energy | Proteinbench clashes inner | Proteinbench clashes outer | Proteinbench cn score | Proteinbench phr | Proteinbench seqnat | Proteinbench seqsim inner | Proteinbench seqsim outer | Proteinbench total energy | RMSD (cdr-h3, ca atoms) | Scrmsd | Sequence recovery (cdr-h3) | TM score (cdr-h3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AbDPOEvaluation | ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy | 116.06 ± 186.06 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-ACCURACY-AAR: Accuracy AAR | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 31.29% ± 7.29 | Not reported |
| AbDPOEvaluation | ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 2.79 ± 3.01 | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.35 ± 0.06 |
| AbDPOEvaluation | ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner | Not reported | 4.14 ± 1.84 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer | Not reported | Not reported | 0 .10 ± 0.24 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score | Not reported | Not reported | Not reported | 1.33 ± 2.31 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-RATIONALITY-SCRMSD: Rationality scRMSD | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 2.79 ± 3.25 | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat | Not reported | Not reported | Not reported | Not reported | Not reported | -1.99 ± 0.34 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 270.12 ± 217.45 | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-SPECIFICITY-PHR: Specificity PHR | Not reported | Not reported | Not reported | Not reported | 69.69% ± 8.49 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0 .60 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AbDPOEvaluation | ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0 .38 | Not reported | Not reported | Not reported | Not reported | Not reported |
All 13 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AbDPO | Task: ProteinBench AB-ACCURACY-AAR: Accuracy AAR Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 31.29% ± 7.29 Sequence recovery (cdr-h3) percent · higher Uncertainty: SD 7.29 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-ACCURACY-AAR: Accuracy AAR Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Accuracy AAR ↑) |
| Configuration: AbDPO | Task: ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 2.79 ± 3.01 RMSD (cdr-h3, ca atoms) unit-unreported · lower Uncertainty: SD 3.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Accuracy RMSD ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 0.35 ± 0.06 TM score (cdr-h3) unitless · higher Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Accuracy TM-score ↑) |
| Configuration: AbDPO | Task: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 116.06 ± 186.06 Proteinbench binding energy unit-unreported · lower Uncertainty: SD 186.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Functionality Binding Energy ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 4.14 ± 1.84 Proteinbench clashes inner count · lower Uncertainty: SD 1.84 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Rationality Clashes-inner ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 0 .10 ± 0.24 Proteinbench clashes outer count · lower Uncertainty: SD 0.24 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Rationality Clashes-outer ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 1.33 ± 2.31 Proteinbench cn score unit-unreported · higher Uncertainty: SD 2.31 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Rationality CN-score ↑) |
| Configuration: AbDPO | Task: ProteinBench AB-RATIONALITY-SCRMSD: Rationality scRMSD Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 2.79 ± 3.25 Scrmsd unit-unreported · lower Uncertainty: SD 3.25 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-RATIONALITY-SCRMSD: Rationality scRMSD Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Rationality scRMSD ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | -1.99 ± 0.34 Proteinbench seqnat unitless · higher Uncertainty: SD 0.34 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Rationality SeqNat ↑) |
| Configuration: AbDPO | Task: ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 270.12 ± 217.45 Proteinbench total energy unit-unreported · lower Uncertainty: SD 217.45 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Rationality Total Energy ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-SPECIFICITY-PHR: Specificity PHR Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 69.69% ± 8.49 Proteinbench phr percent · lower Uncertainty: SD 8.49 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-SPECIFICITY-PHR: Specificity PHR Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Specificity PHR ↓) |
| Configuration: AbDPO | Task: ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 0 .60 Proteinbench seqsim inner unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Specificity SeqSim-inner ↑) |
| Configuration: AbDPO | Task: ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) | 0 .38 Proteinbench seqsim outer unitless · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAbDPO on ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer Antibody design on the 55 antibody-antigen complexes of the RAbD set. Aggregation: Not reported proteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Specificity SeqSim-outer ↓) |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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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-abdpo
- areas
- proteins-complexes
- source locator
- Table 6, row(AbDPO)
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
- provenance note
- Protein model evaluated by the ProteinBench authors under their harness.
Related records
- system: AbDPO on ProteinBench AB-ACCURACY-AAR: Accuracy AAR
- system: AbDPO on ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD
- system: AbDPO on ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score
- system: AbDPO on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- system: AbDPO on ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner
- system: AbDPO on ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer
- system: AbDPO on ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score
- system: AbDPO on ProteinBench AB-RATIONALITY-SCRMSD: Rationality scRMSD
- system: AbDPO on ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat
- system: AbDPO on ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy
- system: AbDPO on ProteinBench AB-SPECIFICITY-PHR: Specificity PHR
- system: AbDPO on ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner
- system: AbDPO on ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer