Evaluation

AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026)

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Evaluation results

1 evaluation · 5 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: How well ipTM tracks DockQ on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	0.736 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P19, AF3: ipTM against DockQ for the best-DockQ sample of each complex
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: How well ipTM tracks DockQ on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	-0.027 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P21, AF3: change in ipTM against change in DockQ under saturation sampling
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: How well ipTM tracks DockQ on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	2% proportion percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P19, AF3: share of predictions with ipTM at least 0.5 and DockQ below 0.23 (confident failures, Q2)
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: How well ipTM tracks DockQ on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	28% proportion percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P19, AF3: share of predictions with ipTM below 0.5 and DockQ at least 0.23 (unconfident successes, Q4)
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: How well ipTM tracks DockQ on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	0.888 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AF3 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P19, AF3: ipTM against DockQ for the first sample (sample0) of each complex

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Evaluation procedure

structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration

Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)
Protocol: How well ipTM tracks DockQ on cognate nanobody-antigen complexes
Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration
dataset version: bioRxiv v1 benchmark
split: Mixed: systems inside and outside the tool's training data
inputs: VHH and antigen sequences
adaptation: None
population: 106 cognate complexes
metric implementation: Pearson correlation; DockQ v2.1.3
aggregation: Across complexes
budget: 50 samples per complex

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Mixed: systems inside and outside the tool's training data
Adaptation: None
Scoring implementation: Pearson correlation; DockQ v2.1.3

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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Evidence table

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19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation None Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.aggregation Across complexes Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.budget 50 samples per complex Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.dataset_version bioRxiv v1 benchmark Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.inputs VHH and antigen sequences Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.metric_implementation Pearson correlation; DockQ v2.1.3 Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.population 106 cognate complexes Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.protocol_id structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.comparison.split Mixed: systems inside and outside the tool's training data Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.limitations 1 values Run by authors who did not develop the tool. Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19 and P21, values for 'AF3' Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed Retrieved: 2026-10-09T21:25:48Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.limitations` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

1 source records and release history

Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Original source · bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed

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Technical metadata and extraction receipts

Stable ID: structural-20261009-eval-smorodina2026-vhh-iptm-dockq-calibration-af3

areas: proteins-complexes
contexts: research
origin: independent_paper
protocol: structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration
version: Primary source as retrieved 2026-10-09
comparison: protocol id: structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration; dataset version: bioRxiv v1 benchmark; split: Mixed: systems inside and outside the tool's training data; inputs: VHH and antigen sequences; adaptation: None; population: 106 cognate complexes; metric implementation: Pearson correlation; DockQ v2.1.3; aggregation: Across complexes; budget: 50 samples per complex
source locator: Results P19 and P21, values for 'AF3'
limitations: Run by authors who did not develop the tool.

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