Relevance of structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled to "Which predicted interfaces or structures are reliable enough to guide my next experiment?"
- Use case
- Choose structural hypotheses to guide experiments
- Assessed by
- Telling cognate from shuffled nanobody-antigen pairs by ipTM
- Relevance
- Proxy evidence
- Endpoint
- Average precision for ranking cognate above shuffled nanobody-antigen pairings by ipTM, for AlphaFold3, Chai-1 and Boltz-2, against a random baseline of about 0.011
Tests the use case's second exclusion directly: whether high confidence indicates that an interaction exists. Proxy evidence: the negatives are pairings assumed not to bind, never tested, and the set mixes training and held-out systems.
3 reviewed evaluations
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.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
| Comparison group nanobody-antigen-interfaces Context-only references | Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
| Comparison title Nanobody-antigen interface predictions (preprint) Context-only references | Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
Constraints4 values
| Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
| Endpoint Average precision for ranking cognate above shuffled nanobody-antigen pairings by ipTM, for AlphaFold3, Chai-1 and Boltz-2, against a random baseline of about 0.011 Context-only references | Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
| Claimed field links:assessed_by:structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled Context-only references | Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
| Headline metric average-precision Context-only references | Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
Limitations8 values
| Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
Pinned records9 values
| Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
| Rationale Tests the use case's second exclusion directly: whether high confidence indicates that an interaction exists. Proxy evidence: the negatives are pairings assumed not to bind, never tested, and the set mixes training and held-out systems. Context-only references | Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2 Version: bioRxiv version 1, posted 2026-03-03; Europe PMC preprint full text PPR1221387 (manuscript EMS215481); not peer reviewed | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: JATS XML parse (xml.etree), by extract/extract_structural.py |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record 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: use-case-mapping-structural-20261009-smorodina2026-cognate-vs-shuffled
- field
- links:assessed_by:structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled
- value
- structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled
- relevance
- proxy
- endpoint
- Average precision for ranking cognate above shuffled nanobody-antigen pairings by ipTM, for AlphaFold3, Chai-1 and Boltz-2, against a random baseline of about 0.011
- rationale
- Tests the use case's second exclusion directly: whether high confidence indicates that an interaction exists. Proxy evidence: the negatives are pairings assumed not to bind, never tested, and the set mixes training and held-out systems.
- constraints
- Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; complex sets, sampling and metrics differ.; Results for one complex class do not establish performance in another.; Structural accuracy and confidence are not evidence that an interaction exists, how strong it is or that an experiment will work.
- 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.
- citation locators
- source id: structural-20261009-source-smorodina2026; locator: Results P9 to P11; Figure 2
- source locator
- structural-20261009-source-smorodina2026: Results P9 to P11; Figure 2
- revision
- 1
- reason
- Add comparisons of structure-prediction reliability by complex class from the structural hypotheses use-case pass 2026-10-09.
- comparison group
- nanobody-antigen-interfaces
- comparison title
- Nanobody-antigen interface predictions (preprint)
- headline metric
- average-precision
- stratum label
- Confidence as evidence of binding
- stratum order
- 3
- reviewed evaluations
- structural-20261009-eval-smorodina2026-vhh-cognate-vs-shuffled-af3; structural-20261009-eval-smorodina2026-vhh-cognate-vs-shuffled-boltz2; structural-20261009-eval-smorodina2026-vhh-cognate-vs-shuffled-chai1
- review
- method: automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; reviewed at: 2026-10-10T00:30:00Z; note: Independent review of endpoint fit, relevance grade, limitations, exclusions and grouping against the use case and the preprint; every value of the listed evaluations was checked against the paragraph its locator names. Preprint; no execution, reproduction, human scientific review or clinical validation.
- pins
- record id: structural-20261009-eval-smorodina2026-vhh-cognate-vs-shuffled-af3; fields: status; links; attributes.origin; attributes.comparison; sha256: e8e5e5381e3f475d58565bf91a56e1f3eb8f3959f9c946d63c413ce1b6e33802; record id: structural-20261009-eval-smorodina2026-vhh-cognate-vs-shuffled-boltz2; fields: status; links; attributes.origin; attributes.comparison; sha256: ab07e5fc17f06dbe78280f3bd25ff1ad39c0eecf074e65086458f746e7ecc74b; record id: structural-20261009-eval-smorodina2026-vhh-cognate-vs-shuffled-chai1; fields: status; links; attributes.origin; attributes.comparison; sha256: 3c1047b90b496350603401946a960bb7008c6912f3e6e108e07657112ada306f; record id: structural-20261009-protocol-smorodina2026-vhh-cognate-vs-shuffled; fields: status; name; description; facets; source_ids; links; attributes; sha256: 1731cd84636045e49aea4a986346bd5a9572b10cf95114dd25719fd6dfb1e3fe; record id: structural-20261009-result-smorodina2026-vhh-cognate-vs-shuffled-af3-average-precision; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 39fda4c791bb7800960fbb92e19b140a4da412457977e1629fae7f588d2b7f3b; record id: structural-20261009-result-smorodina2026-vhh-cognate-vs-shuffled-boltz2-average-precision; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 4b4995df9b0bd5bdfb045ec8a68a2c021aa7343b658e385df81a5f5909006f7d; record id: structural-20261009-result-smorodina2026-vhh-cognate-vs-shuffled-chai1-average-precision; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: ac0b501100172ad0f881656b6fb380ff1fb46f15ac251a9a19f8e2b6f7e8f1ae; record id: structural-20261009-source-smorodina2026; fields: status; attributes.artifact_sha256; sha256: 36153b6f7f2004b2450c64593497cffb16a6fe6676875e5b986458cef5c96d93; record id: use-case-structural-hypotheses-experiments; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 323c287cae7885e983feb5d58f24115afe49ecfbb868a0238c75b1247ffcf228