Result

0.493 pearson-correlation

smorodina2026-vhh-iptm-dockq-calibration-boltz2 pearson-correlation

Tested 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
Procedure: structural-20261009-protocol-smorodina2026-vhh-iptm-dockq-calibration
Evaluation: Boltz-2 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedStructural 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

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

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.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row 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
Reported result 0.493 Individual claims	Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores Original source ↗ Results P19, Boltz-2: ipTM against DockQ for the first sample (sample0) of each complex 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	source checked ["source-hash-verification","transcription","independent-cell-check"] · 2026-10-09 independent paper Audit details Extracted by regular expressions over the Results paragraphs of the JATS XML, each asserted to match exactly once, with the discussion's rounded repeat checked against the Results values. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py Inspected artifact Extraction artifact SHA-256: `0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732` Extraction 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-result-smorodina2026-vhh-iptm-dockq-calibration-boltz2-sample0

metric: pearson-correlation
metric qualifier: ipTM against DockQ for the first sample (sample0) of each complex
metric direction: higher
unit: unitless
printed value: 0.493
numeric value: 0.493
source locator: Results P19, Boltz-2: ipTM against DockQ for the first sample (sample0) of each complex
review: method: source-hash-verification; transcription; independent-cell-check; method note: Re-downloaded the article XML and matched its SHA-256. Extracted the paragraphs with a separate parser and checked the printed value, numeric value, tool label, metric, qualifier, unit and direction against the exact paragraph the locator names. Paragraph numbers count every paragraph of the article, which is the scheme the batch uses throughout.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 0ad24054d98fd1888fa8bf3120f76e22f7bf6b1965261b16f045986d72c50732; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PPR1221387/fullTextXML; note: Extracted by regular expressions over the Results paragraphs of the JATS XML, each asserted to match exactly once, with the discussion's rounded repeat checked against the Results values. Independent review 2026-10-09: value and identity match the source.
missing metadata: uncertainty: reason: unreported

Related records

evaluation: Boltz-2 on How well ipTM tracks DockQ on cognate nanobody-antigen complexes (Smorodina et al. 2026)

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