ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
Functionality Binding Energy. Scored with Binding Energy on RAbD, 55 antibody-antigen complexes. Antibody design on the 55 antibody-antigen complexes of the RAbD set.
Overview
Functionality Binding Energy. Scored with Binding Energy on RAbD, 55 antibody-antigen complexes. Antibody design on the 55 antibody-antigen complexes of the RAbD set.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AbDPO on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- AbDPO++ on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- DiffAb on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- dyMEAN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- dyMEAN-FixFR on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- HERN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- MEAN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- RAbD (natural) on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
binding-energy (score) · Lower values are better for this metric.
Every method ProteinBench reports on Functionality Binding Energy, scored with Binding Energy on RAbD, 55 antibody-antigen complexes.
Evaluation protocol · RAbD, 55 antibody-antigen complexes (ProteinBench split)
- RAbD (natural) · Configuration · Author-reported evaluation-15.33
- HERN · Configuration · Author-reported evaluation1242.77
- MEAN · Configuration · Author-reported evaluation263.90
- dyMEAN · Configuration · Author-reported evaluation889.28
- dyMEAN-FixFR · Configuration · Author-reported evaluation612.75 ± 56.03
- DiffAb · Configuration · Author-reported evaluation489.42 ± 499.76
- AbDPO · Configuration · Author-reported evaluation116.06 ± 186.06
- AbDPO++ · Configuration · Author-reported evaluation2 23.73 ± 281.7
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
proteinbench primary benchmark evidence · Table 6, column(Functionality Binding Energy ↓)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| RAbD (natural) · Configuration | -15.33 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(RAbD (natural)), column(Functionality Binding Energy ↓) |
| HERN · Configuration | 1242.77 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(HERN), column(Functionality Binding Energy ↓) |
| MEAN · Configuration | 263.90 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(MEAN), column(Functionality Binding Energy ↓) |
| dyMEAN · Configuration | 889.28 score | Not reported | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(dyMEAN), column(Functionality Binding Energy ↓) |
| dyMEAN-FixFR · Configuration | 612.75 ± 56.03 score | type: standard_deviation; value: 56.03 | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(dyMEAN-FixFR), column(Functionality Binding Energy ↓) |
| DiffAb · Configuration | 489.42 ± 499.76 score | type: standard_deviation; value: 499.76 | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(DiffAb), column(Functionality Binding Energy ↓) |
| AbDPO · Configuration | 116.06 ± 186.06 score | type: standard_deviation; value: 186.06 | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Functionality Binding Energy ↓) |
| AbDPO++ · Configuration | 2 23.73 ± 281.7 score | type: standard_deviation; value: 281.7 | Author-reported evaluation · source checkedproteinbench primary benchmark evidence · Table 6, row(AbDPO++), column(Functionality Binding Energy ↓) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- Many of these metrics are better when lower, including scRMSD, perplexity and binding energy. The direction comes from the arrow in the paper's own header.
- Rows such as Native PDBs and RAbD are the natural reference the authors include for scale, not a competing method.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 8 evaluations · 8 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AbDPO on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: AbDPOTask: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 116.06 ± 186.06 binding-energy Unit: score · Direction: lower | Uncertainty: type: standard deviation; value: 186.06 Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(AbDPO), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| AbDPO++ on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: AbDPO++Task: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 2 23.73 ± 281.7 binding-energy Unit: score · Direction: lower | Uncertainty: type: standard deviation; value: 281.7 Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(AbDPO++), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| DiffAb on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: DiffAbTask: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 489.42 ± 499.76 binding-energy Unit: score · Direction: lower | Uncertainty: type: standard deviation; value: 499.76 Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(DiffAb), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| dyMEAN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: dyMEANTask: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 889.28 binding-energy Unit: score · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(dyMEAN), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| dyMEAN-FixFR on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: dyMEAN-FixFRTask: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 612.75 ± 56.03 binding-energy Unit: score · Direction: lower | Uncertainty: type: standard deviation; value: 56.03 Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(dyMEAN-FixFR), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| HERN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: HERNTask: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1242.77 binding-energy Unit: score · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(HERN), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| MEAN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: MEANTask: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| 263.90 binding-energy Unit: score · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(MEAN), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
| RAbD (natural) on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy Configuration: RAbD (natural)Task: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding EnergyDataset subset: RAbD, 55 antibody-antigen complexes (ProteinBench split) Antibody design on the 55 antibody-antigen complexes of the RAbD set. Author-reported evaluation · Evaluation metadata: source checked | ||
| -15.33 binding-energy Unit: score · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedproteinbench primary benchmark evidence · Table 6, row(RAbD (natural)), column(Functionality Binding Energy ↓) Source checking is not independent reproduction. |
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-proteinbench Individual claims | proteinbench primary benchmark evidence Table 6, column(Functionality Binding Energy ↓) Version: 2409.06744v1 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: proteinbench-association-ab-functionality-binding-energy Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- proteinbench primary benchmark evidence · Original source · 2409.06744v1
Technical metadata and extraction receipts
Stable ID: proteinbench-task-ab-functionality-binding-energy
- areas
- proteins-complexes
- tasks
- Functionality Binding Energy
- metric
- Binding Energy
- metric direction
- lower
- dataset
- RAbD, 55 antibody-antigen complexes
- protocol
- Antibody design on the 55 antibody-antigen complexes of the RAbD set.
- source locator
- Table 6, column(Functionality Binding Energy ↓)
- comparison panels
- id: proteinbench-panel-ab-functionality-binding-energy; title: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy; protocol id: proteinbench-task-ab-functionality-binding-energy; dataset id: proteinbench-dataset-rabd-55-antibody-antigen-complexes; metric: binding-energy; unit: score; direction: lower; result ids: proteinbench-result-rabd-natural-ab-functionality-binding-energy-binding-energy; proteinbench-result-hern-ab-functionality-binding-energy-binding-energy; proteinbench-result-mean-ab-functionality-binding-energy-binding-energy; proteinbench-result-dymean-ab-functionality-binding-energy-binding-energy; proteinbench-result-dymean-fixfr-ab-functionality-binding-energy-binding-energy; proteinbench-result-diffab-ab-functionality-binding-energy-binding-energy; proteinbench-result-abdpo-ab-functionality-binding-energy-binding-energy; proteinbench-result-abdpo-plus-plus-ab-functionality-binding-energy-binding-energy; source ids: expansion-p3-proteinbench; source locator: Table 6, column(Functionality Binding Energy ↓); context: Every method ProteinBench reports on Functionality Binding Energy, scored with Binding Energy on RAbD, 55 antibody-antigen complexes.; caveats: Author-reported numbers, source checked but not independently reproduced.; Many of these metrics are better when lower, including scRMSD, perplexity and binding energy. The direction comes from the arrow in the paper's own header.; Rows such as Native PDBs and RAbD are the natural reference the authors include for scale, not a competing method.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: ProteinBench
- subject: ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: part of discovery-benchmark-proteinbench
- benchmark: AbDPO on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: AbDPO++ on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: DiffAb on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: dyMEAN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: dyMEAN-FixFR on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: HERN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: MEAN on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy
- benchmark: RAbD (natural) on ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy