Model type
Biomolecular structure predictor; this record is the paper-specific evaluated configuration.
Configuration
Boltz-1
Boltz-1 predicts three-dimensional biomolecular complexes with an atom-coordinate diffusion model.
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · Modeling/Confidence model (paragraph 2); Boltz steering/Method (paragraph 5)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
Boltz-1 Democratizing Biomolecular Interaction Modeling · Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2)At a glance
Biological inputs
Protein, RNA or DNA sequences and small-molecule identities, with the model’s sequence and structural preprocessing
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · Results (paragraph 1); Data pipeline/Validation and test sets curation (paragraph 4)Outputs
Three-dimensional complexes and confidence estimates
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · Results/Evaluation criteria (paragraph 2); Results/Results (paragraph 2)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 |
|---|---|---|
| Boltz-1: Protein–ligand pose prediction Highest-confidence pose from five samples; precomputed MSAs up to 4,096 sequences. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.545 Top-1 ligand RMSD <2 Å rate Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedBoltz-1 Democratizing Biomolecular Interaction Modeling · Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column Source checking is not independent reproduction. |
How it works
How the evaluated method works
A token-and-pair representation trunk conditions a multiresolution transformer that denoises atom coordinates. The confidence model reuses trunk components, including a 48-layer PairFormer, to assess the generated structure.
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2)Underlying method and version boundaries
The official Boltz repository publishes separate Boltz-1 and Boltz-2 models. Boltz-2 adds affinity prediction and other changes; these are not retroactively attributed to Boltz-1 evaluations.
Sources
jwohlwend/boltz README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies Boltz-1: Protein–ligand pose prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-039Strengths and limitations
Strengths and considerations
- Publishes model weights and training/inference implementation, allowing inspection of the structure-prediction procedure.
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · Modeling/Confidence model/Overall procedure and training (paragraph 1); Modeling/Training and inference procedures/Kabsch diffusion interpolation (paragraph 3)
Limitations and conditions
- Atom-coordinate generation can produce stereochemical violations; confidence estimates do not replace checks of physical plausibility.
Sources
Boltz-1 Democratizing Biomolecular Interaction Modeling · Results/Results (paragraph 4); Modeling/Confidence model (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-4058c43eb73b90Specifications
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 | Biomolecular structure predictor; this record is the paper-specific evaluated configuration.Sourcesjwohlwend/boltz README.md · README.md model description |
| Architecture / procedure | A token-and-pair representation trunk conditions a multiresolution transformer that denoises atom coordinates. The confidence model reuses trunk components, including a 48-layer PairFormer, to assess the generated structure.SourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2) |
| Biological inputs | Protein, RNA or DNA sequences and small-molecule identities, with the model’s sequence and structural preprocessingSourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Results (paragraph 1); Data pipeline/Validation and test sets curation (paragraph 4) |
| Outputs | Three-dimensional complexes and confidence estimatesSourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Results/Evaluation criteria (paragraph 2); Results/Results (paragraph 2) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Boltz-1 Democratizing Biomolecular Interaction Modeling; jwohlwend/boltz README.md · Data pipeline/Data source and processing/Structure prediction training pipeline; Modeling/Architectural modifications/MSA module; Modeling/Architectural modifications/Transformer layer; Modeling/Training and inference procedures/Kabsch diffusion interpolation; Modeling/Training and inference procedures/Diffusion loss weighting; Modeling/Confidence model/Trunk architecture and initialization; Modeling/Confidence model/Overall procedure and training; Boltz steering/Method; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | 3 recycling rounds; 200 diffusion stepsSourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Table T4 (paragraph 1); Results/Baselines (paragraph 2) |
| Training data / fitting | PDB structures and an OpenFold distillation dataset of approximately 270,000 structures; the last training stage uses PDB structures only.SourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Data pipeline/Data source and processing/Structure prediction training pipeline (paragraph 1); Modeling/Training and inference procedures/Kabsch diffusion interpolation (paragraph 3) |
| Context limits | Training crops use 384 then 512 tokens and 3,456 then 4,608 atoms; these are training crop sizes, not declared inference maxima.SourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Data pipeline/Unified cropping algorithm (paragraph 1); Modeling/Optimizations/Sequence-local atom representation (paragraph 1) |
| Access | Official upstream implementation and usage documentation: https://github.com/jwohlwend/boltz/blob/b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesjwohlwend/boltz README.md · README.md; installation, model download and usage instructions |
| Code licence | MIT (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesjwohlwend/boltz LICENSE · LICENSE; complete licence text |
| Weights licence | MIT, as explicitly stated in the paper for the released weights.SourcesBoltz-1 Democratizing Biomolecular Interaction Modeling · Results/Baselines (paragraph 1); Boltz steering/Method (paragraph 6) |
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 | Boltz-1 Democratizing Biomolecular Interaction Modeling Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2) Version: PMC archival version PMC11601547.4 | 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 ["Protein, RNA or DNA sequences and small-molecule identities, with the model’s sequence and structural preprocessing","Boltz-1","Three-dimensional complexes and confidence estimates"] Individual claims | Boltz-1 Democratizing Biomolecular Interaction Modeling Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2) Version: PMC archival version PMC11601547.4 | 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 | Boltz-1 Democratizing Biomolecular Interaction Modeling Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2) Version: PMC archival version PMC11601547.4 | 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 Biomolecular structure predictor; this record is the paper-specific evaluated configuration. Individual claims | jwohlwend/boltz README.md README.md model description Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | 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 A token-and-pair representation trunk conditions a multiresolution transformer that denoises atom coordinates. The confidence model reuses trunk components, including a 48-layer PairFormer, to assess the generated structure. Individual claims | Boltz-1 Democratizing Biomolecular Interaction Modeling Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2) Version: PMC archival version PMC11601547.4 | 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 MIT, as explicitly stated in the paper for the released weights. Individual claims | Boltz-1 Democratizing Biomolecular Interaction Modeling Results/Baselines (paragraph 1); Boltz steering/Method (paragraph 6) Version: PMC archival version PMC11601547.4 | 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 |
| Biological inputs Protein, RNA or DNA sequences and small-molecule identities, with the model’s sequence and structural preprocessing Individual claims | Boltz-1 Democratizing Biomolecular Interaction Modeling Results (paragraph 1); Data pipeline/Validation and test sets curation (paragraph 4) Version: PMC archival version PMC11601547.4 | 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 Three-dimensional complexes and confidence estimates Individual claims | Boltz-1 Democratizing Biomolecular Interaction Modeling Results/Evaluation criteria (paragraph 2); Results/Results (paragraph 2) Version: PMC archival version PMC11601547.4 | 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 | Boltz-1 Democratizing Biomolecular Interaction Modeling Data pipeline/Data source and processing/Structure prediction training pipeline; Modeling/Architectural modifications/MSA module; Modeling/Architectural modifications/Transformer layer; Modeling/Training and inference procedures/Kabsch diffusion interpolation; Modeling/Training and inference procedures/Diffusion loss weighting; Modeling/Confidence model/Trunk architecture and initialization; Modeling/Confidence model/Overall procedure and training; Boltz steering/Method; 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 PMC11601547.4 | 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 | jwohlwend/boltz README.md Data pipeline/Data source and processing/Structure prediction training pipeline; Modeling/Architectural modifications/MSA module; Modeling/Architectural modifications/Transformer layer; Modeling/Training and inference procedures/Kabsch diffusion interpolation; Modeling/Training and inference procedures/Diffusion loss weighting; Modeling/Confidence model/Trunk architecture and initialization; Modeling/Confidence model/Overall procedure and training; Boltz steering/Method; 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: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | 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
- Boltz-1 Democratizing Biomolecular Interaction Modeling · Original source · PMC archival version PMC11601547.4
- jwohlwend/boltz README.md · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- jwohlwend/boltz LICENSE · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
Technical metadata and extraction receipts
Stable ID: reported-model-4058c43eb73b90
- areas
- molecular-interactions
- entity level
- method
- version
- 3 recycling rounds; 200 diffusion steps
- reported name
- Boltz-1
- historical missing metadata
- 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: boltz1-2025; evidence-reported-base-boltz-readme-md; source locator: Modeling/Confidence model (paragraph 2); Modeling/Optimizations/Attention bias sharing and caching (paragraph 2) | README.md model description | Modeling/Confidence model (paragraph 2); Boltz steering/Method (paragraph 5); 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.