Telling cognate from shuffled nanobody-antigen pairs by ipTM
All-against-all VHH-antigen pairings are predicted; the best ipTM of 50 samples ranks each pairing, scored by average precision for the cognate pairs.
Overview
All-against-all VHH-antigen pairings are predicted; the best ipTM of 50 samples ranks each pairing, scored by average precision for the cognate pairs.
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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
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- 3
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Evidence
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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source · bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed
Technical metadata and extraction receipts
Stable ID: structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled
- areas
- proteins-complexes
- contexts
- research
- protocol
- Each VHH is paired with each antigen over 91 unique PDB entries and predicted with 50 samples per pairing. Each pairing is scored by its interface confidence (ipTM). Precision-recall over all pairings, with the cognate pairing as the positive, summarised as average precision.
- version
- Smorodina et al. 2026 bioRxiv v1, Results P8 to P11, Figure 2B
- metric
- average-precision
- metric direction
- higher
- unit
- unitless
- metric definition
- Area under the precision-recall curve (average precision) for ranking cognate pairs above shuffled pairs by ipTM. The random baseline equals the positive prevalence, printed as about 0.011.
- limitations
- Negatives are shuffled pairings assumed to be non-binders; none was tested, and some may bind.; Ranks pairings by ipTM; it measures whether confidence separates observed from assumed-absent interactions, not structural accuracy.; Nanobody (VHH)-antigen complexes only; results do not transfer to conventional antibodies or other complex classes.; The set mixes systems inside and outside each tool's training data (AF3 30 of 106 in training, Chai-1 25, Boltz-2 64); the printed values are over all systems, so they are not post-cutoff results, and Boltz-2's are the most exposed.; Preprint, not peer reviewed. Supplementary tables were not read.; No uncertainty is printed for these values.; The dataset paragraph (P62) says post-October 2021 depositions were kept, 'corresponding to the earliest training cutoff among the evaluated tools (Boltz-2)'. The methods (P76) give Chai-1 about 12 January 2021, AF3 about 30 September 2021 and Boltz-2 about 1 June 2023, so Chai-1 is the earliest and Boltz-2 the latest, and the October 2021 date matches AF3. The per-tool train and test counts follow the methods, and no printed value depends on the mis-stated sentence.; Preprint, not peer reviewed.; The abstract gives 11,342 shuffled pairings; Results P8 gives 11,130 (106 squared minus 106). Neither figure is used in a stored value; the scored counts come from Results P11.
- source locator
- Results P8 to P11; Figure 2
Related records
- uses data: Smorodina et al. 2026 all-against-all VHH-antigen pairing matrix (91 unique PDB entries)
- subject: baseline: structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled
- subject: negative_definition: structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled
- assessment: AF3 on Telling cognate from shuffled nanobody-antigen pairs by ipTM (Smorodina et al. 2026)
- assessment: Boltz-2 on Telling cognate from shuffled nanobody-antigen pairs by ipTM (Smorodina et al. 2026)
- assessment: Chai-1 on Telling cognate from shuffled nanobody-antigen pairs by ipTM (Smorodina et al. 2026)
- assessed by: Choose structural hypotheses to guide experiments