Dataset

Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes

Experimentally determined nanobody-antigen complexes, used as the real (cognate) systems.

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Release 2026-10-10-6e93f504adfc · Evidence verified: Not verified

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Evaluation results

7 evaluations · 20 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: 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: Boltz-1 via Boltz CLI v2.2.0, MSA server (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	0.06 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 Boltz-1 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, Boltz-1 (0.06 to 0.26), N = 1
Configuration: Boltz-1 via Boltz CLI v2.2.0, MSA server (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	0.26 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 Boltz-1 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, Boltz-1 (0.06 to 0.26), N = 100
Configuration: Boltz-2 via Boltz CLI v2.2.0, 50 diffusion samples, seed 42, MSA server (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	0.57 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 Boltz-2 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, Boltz-2 (0.57 to 0.80), N = 1
Configuration: Boltz-2 via Boltz CLI v2.2.0, 50 diffusion samples, seed 42, MSA server (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	0.8 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 Boltz-2 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, Boltz-2 (0.57 to 0.80), N = 100
Configuration: Chai-1 0.6.1, 5 trunk x 10 diffusion samples, seed 42, ESM embeddings without MSAs (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	0.04 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 Chai-1 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, Chai-1 (0.04 to 0.19), N = 1
Configuration: Chai-1 0.6.1, 5 trunk x 10 diffusion samples, seed 42, ESM embeddings without MSAs (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	0.19 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 Chai-1 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, Chai-1 (0.04 to 0.19), 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
Configuration: Boltz-2 via Boltz CLI v2.2.0, 50 diffusion samples, seed 42, MSA server (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	0.665 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 Boltz-2 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, Boltz-2: ipTM against DockQ for the best-DockQ sample of each complex
Configuration: Boltz-2 via Boltz CLI v2.2.0, 50 diffusion samples, seed 42, MSA server (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	-0.04 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 Boltz-2 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, Boltz-2: change in ipTM against change in DockQ under saturation sampling
Configuration: Boltz-2 via Boltz CLI v2.2.0, 50 diffusion samples, seed 42, MSA server (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	18% 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 Boltz-2 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, Boltz-2: share of predictions with ipTM at least 0.5 and DockQ below 0.23 (confident failures, Q2)
Configuration: Boltz-2 via Boltz CLI v2.2.0, 50 diffusion samples, seed 42, MSA server (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	0.493 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 Boltz-2 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, Boltz-2: ipTM against DockQ for the first sample (sample0) of each complex
Configuration: Chai-1 0.6.1, 5 trunk x 10 diffusion samples, seed 42, ESM embeddings without MSAs (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	0.612 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 Chai-1 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, Chai-1: ipTM against DockQ for the best-DockQ sample of each complex
Configuration: Chai-1 0.6.1, 5 trunk x 10 diffusion samples, seed 42, ESM embeddings without MSAs (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	-0.019 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 Chai-1 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, Chai-1: change in ipTM against change in DockQ under saturation sampling
Configuration: Chai-1 0.6.1, 5 trunk x 10 diffusion samples, seed 42, ESM embeddings without MSAs (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	24% 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 Chai-1 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, Chai-1: share of predictions with ipTM below 0.5 and DockQ at least 0.23 (unconfident successes, Q4)

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

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Inspect claims, sources and review details

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7 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.population 106 VHH-antigen systems from 91 PDB entries; 15 entries hold two VHHs bound to different epitopes Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `attributes.population` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.scope_note Curated from SAbDab-nano (downloaded March 2025; post-October 2021 depositions) and from AACDB, whose pre-cutoff structures were kept on purpose to probe memorisation. Resolution 3.0 Å or better, VHH 110 to 150 residues, antigen 100 to 400 residues. Per-tool training overlap printed by the source: AF3 30 train and 76 test systems, Chai-1 25 and 81, Boltz-2 64 and 42. Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `attributes.scope_note` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.source_locator Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `attributes.source_locator` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.total 106 Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `attributes.total` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
attributes.version bioRxiv v1 benchmark; Zenodo 10.5281/zenodo.18390239 Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `attributes.version` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
description Experimentally determined nanobody-antigen complexes, used as the real (cognate) systems. Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `description` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact
name Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes Context-only references	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76 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 Audit details Field: `name` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact

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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-data-smorodina2026-vhh-antigen-106

areas: proteins-complexes
contexts: research
version: bioRxiv v1 benchmark; Zenodo 10.5281/zenodo.18390239
population: 106 VHH-antigen systems from 91 PDB entries; 15 entries hold two VHHs bound to different epitopes
total: 106
scope note: Curated from SAbDab-nano (downloaded March 2025; post-October 2021 depositions) and from AACDB, whose pre-cutoff structures were kept on purpose to probe memorisation. Resolution 3.0 Å or better, VHH 110 to 150 residues, antigen 100 to 400 residues. Per-tool training overlap printed by the source: AF3 30 train and 76 test systems, Chai-1 25 and 81, Boltz-2 64 and 42.
source locator: Methods, VHH-antigen dataset curation (P62 and following); Results P13; Methods P76

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