DiffAb | configuration

Overview

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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)
DiffAbEvaluation	ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy	489.42 ± 499.76	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	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	35.04% ± 8.36	Not reported
DiffAbEvaluation	ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	2.53 ± 0.60	Not reported	Not reported	Not reported
DiffAbEvaluation	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	0.37 ± 0.06
DiffAbEvaluation	ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner	Not reported	1 .84 ± 1.35	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer	Not reported	Not reported	0.19 ± 0.31	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score	Not reported	Not reported	Not reported	2 .02 ± 2.83	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	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	2.57 ± 0.77	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat	Not reported	Not reported	Not reported	Not reported	Not reported	-1.88 ± 0.47	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	495.69 ± 350.96	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-SPECIFICITY-PHR: Specificity PHR	Not reported	Not reported	Not reported	Not reported	40.68% ± 10.65	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.45	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DiffAbEvaluation	ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.37	Not reported	Not reported	Not reported	Not reported	Not reported

All 13 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DiffAb	Task: ProteinBench AB-ACCURACY-AAR: Accuracy AAR Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	35.04% ± 8.36 Sequence recovery (cdr-h3) percent · higher Uncertainty: SD 8.36 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Accuracy AAR ↑)
Configuration: DiffAb	Task: ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	2.53 ± 0.60 RMSD (cdr-h3, ca atoms) unit-unreported · lower Uncertainty: SD 0.60 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Accuracy RMSD ↓)
Configuration: DiffAb	Task: ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	0.37 ± 0.06 TM score (cdr-h3) unitless · higher Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Accuracy TM-score ↑)
Configuration: DiffAb	Task: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	489.42 ± 499.76 Proteinbench binding energy unit-unreported · lower Uncertainty: SD 499.76 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Functionality Binding Energy ↓)
Configuration: DiffAb	Task: ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	1 .84 ± 1.35 Proteinbench clashes inner count · lower Uncertainty: SD 1.35 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Rationality Clashes-inner ↓)
Configuration: DiffAb	Task: ProteinBench AB-RATIONALITY-CLASHES-OUTER: Rationality Clashes-outer Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	0.19 ± 0.31 Proteinbench clashes outer count · lower Uncertainty: SD 0.31 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Rationality Clashes-outer ↓)
Configuration: DiffAb	Task: ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	2 .02 ± 2.83 Proteinbench cn score unit-unreported · higher Uncertainty: SD 2.83 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Rationality CN-score ↑)
Configuration: DiffAb	Task: ProteinBench AB-RATIONALITY-SCRMSD: Rationality scRMSD Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	2.57 ± 0.77 Scrmsd unit-unreported · lower Uncertainty: SD 0.77 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Rationality scRMSD ↓)
Configuration: DiffAb	Task: ProteinBench AB-RATIONALITY-SEQNAT: Rationality SeqNat Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	-1.88 ± 0.47 Proteinbench seqnat unitless · higher Uncertainty: SD 0.47 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Rationality SeqNat ↑)
Configuration: DiffAb	Task: ProteinBench AB-RATIONALITY-TOTAL-ENERGY: Rationality Total Energy Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	495.69 ± 350.96 Proteinbench total energy unit-unreported · lower Uncertainty: SD 350.96 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Rationality Total Energy ↓)
Configuration: DiffAb	Task: ProteinBench AB-SPECIFICITY-PHR: Specificity PHR Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	40.68% ± 10.65 Proteinbench phr percent · lower Uncertainty: SD 10.65 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Specificity PHR ↓)
Configuration: DiffAb	Task: ProteinBench AB-SPECIFICITY-SEQSIM-INNER: Specificity SeqSim-inner Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	0.45 Proteinbench seqsim inner unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Specificity SeqSim-inner ↑)
Configuration: DiffAb	Task: ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer Dataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split)	0.37 Proteinbench seqsim outer unitless · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DiffAb 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(DiffAb), column(Specificity SeqSim-outer ↓)

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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proteinbench primary benchmark evidence · Original source · 2409.06744v1

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Technical metadata and extraction receipts

Stable ID: proteinbench-method-diffab

areas: proteins-complexes
source locator: Table 6, row(DiffAb)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Protein model evaluated by the ProteinBench authors under their harness.

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