Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Configuration
Ibex
Ibex predicts antibody, nanobody and T-cell-receptor structures with an explicit bound/unbound conformation input.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Introduction (paragraph 5); Methods/Data (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · The Ibex model (paragraph 1); Methods/Model (paragraph 2)At a glance
Biological inputs
Immunoglobulin-family variable-region sequences and an apo/holo conformation token
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Methods/Data (paragraph 1); The Ibex model (paragraph 1)Outputs
Predicted three-dimensional structures in the requested conformational state
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Methods/Training (paragraph 1); Results (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. 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. |
How it works
How the evaluated method works
An AlphaFold2-derived network has 16 structure-module blocks. An apo/holo conformation token is supplied with the variable-region sequence and propagated through residual connections.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · The Ibex model (paragraph 1); Methods/Model (paragraph 2)What was evaluated
The linked evaluation record identifies Ibex: Antibody loop structure prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-040Strengths and limitations
Strengths and considerations
- Treats bound and unbound conformations as distinct training conditions rather than conflating them.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Results/Analysis of paired apo/holo structures (paragraph 1); Methods/Data (paragraph 2)
Limitations and conditions
- Specifying a holo token does not supply the actual binding partner or prove the predicted conformation matches a particular complex.
Sources
Conformation-aware structure prediction of antigen-recognizing immune proteins · Methods/Data (paragraph 1); Discussion (paragraph 2)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-2ae5fb0c147618Specifications
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 |
|---|---|
| Model type | Study-specific predictive method; this record is the paper-specific evaluated configuration.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · The Ibex model (paragraph 1); Methods/Model (paragraph 2) |
| Architecture / procedure | An AlphaFold2-derived network has 16 structure-module blocks. An apo/holo conformation token is supplied with the variable-region sequence and propagated through residual connections.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · The Ibex model (paragraph 1); Methods/Model (paragraph 2) |
| Biological inputs | Immunoglobulin-family variable-region sequences and an apo/holo conformation tokenSourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Methods/Data (paragraph 1); The Ibex model (paragraph 1) |
| Outputs | Predicted three-dimensional structures in the requested conformational stateSourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Methods/Training (paragraph 1); Results (paragraph 1) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Conformation-aware structure prediction of antigen-recognizing immune proteins; prescient-design/ibex README.md · Methods/Model; Methods/Data; Methods/Training; Methods/Private dataset generation and characterization; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | Ibex is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Labelled apo and holo structural pairs described in the paper.SourcesConformation-aware structure prediction of antigen-recognizing immune proteins · Methods/Training (paragraph 3); Methods/Training (paragraph 5) |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Conformation-aware structure prediction of antigen-recognizing immune proteins; prescient-design/ibex README.md · Methods/Model; Methods/Data; Methods/Training; Methods/Private dataset generation and characterization; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official study implementation and usage documentation: https://github.com/prescient-design/ibex/blob/2e785563806a3b63600eeaa2107d1254ddf5d196/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesprescient-design/ibex README.md · README.md; installation, model download and usage instructions |
| Code licence | Apache 2.0 (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesprescient-design/ibex LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesprescient-design/ibex README.md · README.md; checkpoint/access documentation and licence scope |
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins The Ibex model (paragraph 1); Methods/Model (paragraph 2) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Immunoglobulin-family variable-region sequences and an apo/holo conformation token","Ibex","Predicted three-dimensional structures in the requested conformational state"] Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins The Ibex model (paragraph 1); Methods/Model (paragraph 2) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins The Ibex model (paragraph 1); Methods/Model (paragraph 2) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins The Ibex model (paragraph 1); Methods/Model (paragraph 2) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure An AlphaFold2-derived network has 16 structure-module blocks. An apo/holo conformation token is supplied with the variable-region sequence and propagated through residual connections. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins The Ibex model (paragraph 1); Methods/Model (paragraph 2) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | prescient-design/ibex README.md README.md; checkpoint/access documentation and licence scope Version: 2e785563806a3b63600eeaa2107d1254ddf5d196 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Immunoglobulin-family variable-region sequences and an apo/holo conformation token Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Methods/Data (paragraph 1); The Ibex model (paragraph 1) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Predicted three-dimensional structures in the requested conformational state Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Methods/Training (paragraph 1); Results (paragraph 1) Version: PMC archival version PMC12710905.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | prescient-design/ibex README.md Methods/Model; Methods/Data; Methods/Training; Methods/Private dataset generation and characterization; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2e785563806a3b63600eeaa2107d1254ddf5d196 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | Conformation-aware structure prediction of antigen-recognizing immune proteins Methods/Model; Methods/Data; Methods/Training; Methods/Private dataset generation and characterization; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC archival version PMC12710905.1 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- Conformation-aware structure prediction of antigen-recognizing immune proteins · Original source · PMC archival version PMC12710905.1
- prescient-design/ibex README.md · Original source · 2e785563806a3b63600eeaa2107d1254ddf5d196
- prescient-design/ibex LICENSE · Original source · 2e785563806a3b63600eeaa2107d1254ddf5d196
Technical metadata and extraction receipts
Stable ID: reported-model-2ae5fb0c147618
- areas
- molecular-interactions
- entity level
- method
- version
- Not reported
- reported name
- Ibex
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: 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
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: ibex-2025; source locator: The Ibex model (paragraph 1); Methods/Model (paragraph 2) | Introduction (paragraph 5); Methods/Data (paragraph 1); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.