AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026); alphafold3-3.0.1

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3 evaluations · 8 results. Different protocols are not a single leaderboard.

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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: Telling cognate from shuffled nanobody-antigen pairs by ipTM Dataset: Smorodina et al. 2026 all-against-all VHH-antigen pairing matrix (91 unique PDB entries)	0.187 average-precision 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 Telling cognate from shuffled nanobody-antigen pairs by ipTM (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P11, 'AP = 0.187' for AF3
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: Best DockQ against sampling depth on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	0.24 dockq 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 Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-dockq-vs-sampling Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P36, AF3 (0.24 to 0.68), N = 1
Configuration: AlphaFold3 3.0.1, 50 diffusion samples, seed 1, built-in data pipeline (Smorodina et al. 2026)	Protocol: Best DockQ against sampling depth on cognate nanobody-antigen complexes Dataset: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes	0.68 dockq 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 Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026) structural-20261009-protocol-smorodina2026-vhh-dockq-vs-sampling Aggregation: Not reported Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores · Results P36, AF3 (0.24 to 0.68), N = 100
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

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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-config-smorodina2026-af3

areas: proteins-complexes
contexts: research
method types: foundation_model
reported name: AF3
foundation model eligible: true
source locator: Methods, structure prediction (P75)
version: alphafold3-3.0.1
parameters: num_diffusion_samples = 50; run_data_pipeline = true; seed = 1; MSAs from the built-in pipeline
training overlap: 30 of 106 cognate systems in the training set; 76 not (AF3 cutoff about 30 September 2021)

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