Datasets
ImmuneBuilder antibody, nanobody and TCR tests; an additional private antibody-structure dataset.
Task
Antibody loop structure prediction
Antibody loop structure assessment uses public ImmuneBuilder tests and a separate private structural collection.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28Overview
Metrics
Mean region-specific RMSD; private-set loop RMSD is also stratified by sequence edit distance.
Allowed inputs
Immune-protein sequence for loop/structure prediction.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Ibex | Task: Antibody loop structure prediction Dataset: ImmuneBuilder antibody test set | 2.72 Mean CDR H3 RMSD Å · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceIbex: Antibody loop structure prediction Backbone RMSD after framework alignment; average over antibody test structures. Aggregation: Not reported Conformation-aware structure prediction of antigen-recognizing immune proteins · Table 1, Antibodies / Ibex row, CDR H3 column |
| Configuration: Chai-1 | Task: Antibody loop structure prediction Dataset: ImmuneBuilder antibody test set | 2.65 Mean CDR H3 RMSD Å · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1: Antibody loop structure prediction Backbone RMSD after framework alignment; one seed and one diffusion trajectory. Aggregation: Not reported Conformation-aware structure prediction of antigen-recognizing immune proteins · Table 1, Antibodies / Chai-1 row, CDR H3 column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
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.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28Recorded evaluations
Each evaluation records what was tested and under which conditions.
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- Training excludes clusters containing public test structures rather than only deleting exact test entries.
Sources
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
Limitations and conditions
- Private evaluation structures limit independent reproducibility. Antigen context is absent in the described private comparison.
Sources
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
Profile review details
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-f3a12dbc0e0439Specifications
Inputs, training, access and other details
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 |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
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 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 2 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Complete raw table acquired. Antibodyloops cannot be pooled withnanobody/TCR cohorts orframeworkRMSD; sixloopregions separate. LowerÅRMSD; nanobodylight-chain N/A retained. Structured extraction pending.
Search and extraction details
source found structured extraction pending
Searches
- Conformation-aware structure prediction of antigen-recognizing immune proteins primary paper benchmark results
Evidence locations
- Table1 region-specific RMSD; antibody/nanobody/TCR blocks
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.
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
| 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 |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- Conformation-aware structure prediction of antigen-recognizing immune proteins · Original source · PMC archival version PMC12710905.1
- Conformation-aware structure prediction of antigen-recognizing immune proteins · Original source · PMC archival version PMC12710905.1
Technical metadata and extraction receipts
Stable ID: reported-task-f3a12dbc0e0439
- areas
- molecular-interactions
- tasks
- Antibody loop structure prediction
- entity level
- task
- version
- Not reported
- task
- Antibody loop structure prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-ibex-2025-caa1109bd5fe; inspected locators: Table1 region-specific RMSD; antibody/nanobody/TCR blocks; searched queries: Conformation-aware structure prediction of antigen-recognizing immune proteins primary paper benchmark results; gaps: Complete raw table acquired. Antibodyloops cannot be pooled withnanobody/TCR cohorts orframeworkRMSD; sixloopregions separate. LowerÅRMSD; nanobodylight-chain N/A retained. Structured extraction pending.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: ibex-2025; source locator: Results: Benchmarking on the ImmuneBuilder test set; Benchmarking on a private dataset; cached text lines 22–28; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: ImmuneBuilder antibody test set
- benchmark: Ibex: Antibody loop structure prediction
- benchmark: Chai-1: Antibody loop structure prediction