Antibody loop structure assessment uses public ImmuneBuilder tests and a separate private structural collection.
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | ImmuneBuilder antibody, nanobody and TCR tests; an additional private antibody-structure dataset.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Splits | Training excludes clusters containing public test structures; the private set is characterized by loop distance to public structures.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Metrics | Mean region-specific RMSD; private-set loop RMSD is also stratified by sequence edit distance.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Baselines | ESMFold, Chai-1, Boltz-1 and specialized immune-protein structure models.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Leakage controls | Boltz-2 is excluded from the public test comparison because its later training cutoff includes much of that test set.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Uncertainty | Chai-1 and Boltz-1 use one seed/trajectory in the public comparison; this is not a repeated-sampling uncertainty analysis.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Entity type | Paper-specific computational evaluation protocol.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Organisms | Antibody, nanobody and T-cell receptor collections.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Assays | Experimentally determined immune-protein structures.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Allowed inputs | Immune-protein sequence for loop/structure prediction.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
| Adaptation | Structure prediction trained with clusters containing public test examples excluded.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
ImmuneBuilder antibody, nanobody and TCR tests; an additional private antibody-structure dataset. Training excludes clusters containing public test structures; the private set is characterized by loop distance to public structures. Mean region-specific RMSD; private-set loop RMSD is also stratified by sequence edit distance. ESMFold, Chai-1, Boltz-1 and specialized immune-protein structure models. Boltz-2 is excluded from the public test comparison because its later training cutoff includes much of that test set. Chai-1 and Boltz-1 use one seed/trajectory in the public comparison; this is not a repeated-sampling uncertainty analysis.
Each evaluation records what was tested and under which conditions.
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Ibex: Antibody loop structure prediction Backbone RMSD after framework alignment; average over antibody test structures. Author-reported evaluation · Evaluation metadata: needs review | ||
| 2.72 Mean CDR H3 RMSD Unit: Å · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedConformation-aware structure prediction of antigen-recognizing immune proteins · Table 1, Antibodies / Ibex row, CDR H3 column Source checking is not independent reproduction. |
| Chai-1: Antibody loop structure prediction Configuration: Chai-1Task: Antibody loop structure predictionDataset: ImmuneBuilder antibody test set Backbone RMSD after framework alignment; one seed and one diffusion trajectory. Independent external evaluation · Evaluation metadata: needs review | ||
| 2.65 Mean CDR H3 RMSD Unit: Å · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedConformation-aware structure prediction of antigen-recognizing immune proteins · Table 1, Antibodies / Chai-1 row, CDR H3 column Source checking is not independent reproduction. |
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Conformation-aware structure prediction of antigen-recognizing immune proteins | PMC archival version PMC12710905.1 | Read source DOI: 10.1080/19420862.2025.2602217 |
source found structured extraction pending
Task-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced.
Stable record: reported-task-f3a12dbc0e0439Trace 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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Immune-protein sequence for loop/structure prediction.","Evaluation: Structure prediction trained with clusters containing public test examples excluded.","Readout: Mean region-specific RMSD; private-set loop RMSD is also stratified by sequence edit distance."] Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets ImmuneBuilder antibody, nanobody and TCR tests; an additional private antibody-structure dataset. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Training excludes clusters containing public test structures; the private set is characterized by loop distance to public structures. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Structure prediction trained with clusters containing public test examples excluded. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Mean region-specific RMSD; private-set loop RMSD is also stratified by sequence edit distance. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines ESMFold, Chai-1, Boltz-1 and specialized immune-protein structure models. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Boltz-2 is excluded from the public test comparison because its later training cutoff includes much of that test set. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty Chai-1 and Boltz-1 use one seed/trajectory in the public comparison; this is not a repeated-sampling uncertainty analysis. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28 Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-f3a12dbc0e0439