Model type
Biomolecular structure predictor family
Configuration
Boltz-1 (MSA)
Boltz predicts biomolecular complex structures; Boltz-2 also predicts binding affinity.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 LimitationsHow it worksBoltz workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 LimitationsOverview
Inputs
Protein, nucleic-acid and ligand specifications in prediction input files.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 LimitationsOutputs
Predicted complex structures and, for supported Boltz-2 inputs, binding-affinity predictions.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 LimitationsAccess
Official project documentation and implementation: https://github.com/jwohlwend/boltz
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitationslimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Boltz-1 (MSA) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 60% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns N’ Poses receptor–ligand co-folding; source benchmark 2,600 systems. Figure 2C reports n=2,573 scored ligands on the intersection where all models produced valid predictions, after excluding undefined SuCOS scores. Multiple ligands in one system are scored independently. Five seeds × five diffusion samples per target; select top candidate by ipTM. Success requires lDDT-PLI >0.8 and BiSyRMSD <2 angstrom. Baselines use 10 recycles and 200 diffusion steps; ESMFold2 uses 10 or 20 loops as labelled and truncated 68-step diffusion. Single-sequence and MSA conditions remain separate. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 7 from left (Boltz-1 (MSA)), exact printed bar label |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Use this model
How it works, versions and access
Related profile: Boltz. This page retains the exact record and its evaluation context.
This configuration
Author-evaluated folding configuration with conditioning and loop count retained from Figure 2C.
- record
- Boltz-1 (MSA)
- configuration
- Not reported
- entity type
- Configuration
How it works
How it works
Boltz-2 first encodes the molecular inputs, alignments and optional templates into token and pair features. A Pairformer trunk updates those features and conditions atom-coordinate diffusion to generate a complex. Separate confidence and affinity modules assess the prediction; affinity classification and regression outputs answer different questions. This describes the Boltz-2 generation; a Boltz-1 result must retain its original checkpoint and prediction procedure.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 LimitationsVersions and reproducibility
Boltz-1 and Boltz-2 are distinct released generations; the catalogue does not select an evaluated checkpoint. The Boltz-2 report describes training crops up to 768 tokens. This is a training-crop size rather than a universal inference maximum; affinity additionally uses a pocket crop.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 LimitationsStrengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- The project distributes prediction code, model weights and training instructions.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations
Limitations and conditions
- Affinity predictions depend on a plausible binding pose and mix biochemical endpoint types. The report notes limited handling of cofactors, water and multimeric binding partners, and substantial variation between assays.
Sources (6)
jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations
Profile review details
Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.
Stable record: discovery-model-boltzSpecifications
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 familySources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Architecture | Boltz-1 and Boltz-2 are separate generations. In the inspected Boltz-2 implementation, molecular/MSA/template embeddings enter a Pairformer trunk, which conditions atom-coordinate diffusion; confidence and affinity are separate output modules.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Inputs | Protein, nucleic-acid and ligand specifications in prediction input files.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Outputs | Predicted complex structures and, for supported Boltz-2 inputs, binding-affinity predictions.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Parameters | A complete parameter total is not stated in the reviewed Boltz-2 architecture report or model constructor; structure, confidence and affinity are separate modules. · Not reported in inspected sourcesSources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Known versions | Boltz-1 and Boltz-2 are distinct released generations; the catalogue does not select an evaluated checkpoint.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Training data | Boltz-2 structure training combines pre-June-2023 PDB entries, MISATO/ATLAS/mdCATH molecular dynamics, and AlphaFold2/Boltz-1 distillation. Separate affinity training uses curated PubChem, ChEMBL, BindingDB, HTS, CeMM and MIDAS evidence with different regression/classification labels.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Training cutoff | Boltz-2 experimental PDB structures were released before 2023-06-01. This is not a shared cutoff for every affinity, MD or distilled resource, nor a Boltz-1 training cutoff.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Context limits | The Boltz-2 report describes training crops up to 768 tokens. This is a training-crop size rather than a universal inference maximum; affinity additionally uses a pocket crop.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Weights licence | MIT; the README explicitly applies this licence to code and model weights.Sources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Access | Official project documentation and implementation: https://github.com/jwohlwend/boltzSources (6)jwohlwend/boltz: README.md; jwohlwend/boltz: docs/prediction.md; jwohlwend/boltz: docs/training.md; jwohlwend/boltz: src/boltz/model/models/boltz2.py; jwohlwend/boltz: scripts/train/configs/full.yaml; boltz2: Journal full-text XML · src/boltz/model/models/boltz2.py: Boltz2.__init__, forward, PairformerModule, AtomDiffusion and AffinityModule; docs/prediction.md: affinity outputs; Boltz-2 report Sections 2 Data, 3 Architecture, 4 Training and 6 Limitations |
| Code licence | MITSourcesjwohlwend/boltz: LICENSE · LICENSE: licence text |
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: family discovery-model-boltz Individual claims | ESMFold2 primary paper v1, Figure 2C Runs N’ Poses Figure 2C Runs N’ Poses, bar label Boltz-1 (MSA); Appendix A.2.10 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | source checked automated source review · 2026-09-23 Audit detailsSource-backed evaluated identity only; no independent reproduction. Field: Claim: esmfold2-2026-runs-n-poses-method-boltz-1-msa-discovery-model-boltz-identity-claim Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · Original source · 10.64898/2026.06.03.729735v1; posted 2026-06-04
Technical metadata and extraction receipts
Stable ID: esmfold2-2026-runs-n-poses-method-boltz-1-msa
- areas
- proteins-complexes
- source locator
- Figure 2C Runs N’ Poses, bar label Boltz-1 (MSA); Appendix A.2.10
- missing metadata
- checkpoint revision: unreported; parameters: unextracted