Best DockQ against sampling depth on cognate nanobody-antigen complexes
For each of 106 cognate complexes, the best DockQ among N samples, summarised as the median over complexes, at N = 1 and N = 100.
Overview
For each of 106 cognate complexes, the best DockQ among N samples, summarised as the median over complexes, at N = 1 and N = 100.
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4 recorded evaluations, 8 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
4 evaluations · 8 results. Different protocols are not a single leaderboard.
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Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AF3 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- Boltz-1 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- Boltz-2 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- Chai-1 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
Baseline coverage
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- External evaluations
- 4
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Null control
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-10-6e93f504adfc. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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-dockq-vs-sampling
- areas
- proteins-complexes
- contexts
- research
- protocol
- Each complex is predicted with five independent seeds at sampling depths N = 1, 10, 25, 50 and 100. For each complex the maximum DockQ at each depth is taken and the median over complexes is printed for N = 1 and N = 100.
- version
- Smorodina et al. 2026 bioRxiv v1, Results P33 to P36, Methods P83 and P91, Figure 5B
- metric
- dockq
- metric direction
- higher
- unit
- unitless
- metric definition
- Median over complexes of the per-complex maximum DockQ among N samples.
- limitations
- Best-of-N DockQ needs the experimental structure to pick the best sample, so it is an upper bound on what a user could select.; Each sampling depth is a separate run with its own seed (seeds 1 to 5 for N = 1, 10, 25, 50 and 100), unlike the single 50-sample runs of the other protocols.; For Chai-1 the smallest depth is 5 samples (5 trunk samples x 1 diffusion sample), so its N = 1 value is the best of 5.; Boltz-1 appears only in this analysis.; 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.
- source locator
- Results P33 to P36; Methods P83 and P91; Figure 5B
Related records
- uses data: Smorodina et al. 2026 nanobody-antigen benchmark: 106 cognate VHH-antigen complexes
- assessment: AF3 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- assessment: Boltz-1 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- assessment: Boltz-2 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- assessment: Chai-1 on Best DockQ against sampling depth on cognate nanobody-antigen complexes (Smorodina et al. 2026)
- assessed by: Choose structural hypotheses to guide experiments