Model type
Biomolecular structure predictor family
Model
Boltz
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.
Outputs
Predicted complex structures and, for supported Boltz-2 inputs, binding-affinity predictions.
Access
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, 2026-09-23. All specifications and missing details
Evaluations and results
9 evaluations · 25 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: Boltz-1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 60.6% chirality percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: percentage of molecules with consistent chirality Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column chirality; footnote a |
| Configuration: Boltz Rc | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.3 angle_rmsd degree · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: unreported in Table 1 footnote Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column angle_rmsd; footnote a |
| Configuration: Boltz R1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 99.8% chirality percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: percentage of molecules with consistent chirality Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column chirality; footnote a |
| Configuration: Boltz-1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.0283 bond_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column bond_rmsd; footnote a |
| Configuration: Boltz-1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.438 angle_rmsd degree · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: unreported in Table 1 footnote Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column angle_rmsd; footnote a |
| Configuration: Boltz Rc | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.407 protein_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a |
| Configuration: Boltz R | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 100% chirality percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: percentage of molecules with consistent chirality Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column chirality; footnote a |
| Configuration: Boltz R1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.897 angle_rmsd degree · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: unreported in Table 1 footnote Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column angle_rmsd; footnote a |
| Configuration: Boltz R | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.41 protein_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column protein_rmsd; footnote a |
| Configuration: Boltz R | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.0448 angle_rmsd degree · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: unreported in Table 1 footnote Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column angle_rmsd; footnote a |
| Configuration: Boltz R | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.0003 bond_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column bond_rmsd; footnote a |
| Configuration: Boltz Rc | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.0215 bond_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column bond_rmsd; footnote a |
| Configuration: Boltz-1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.404 protein_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column protein_rmsd; footnote a |
| Configuration: Boltz R1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.0345 bond_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column bond_rmsd; footnote a |
| Configuration: Boltz R | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 1.38 ligand_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column ligand_rmsd; footnote a |
| Configuration: Boltz Rc | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 1.27 ligand_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column ligand_rmsd; footnote a |
| Configuration: Boltz-1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 1.39 ligand_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column ligand_rmsd; footnote a |
| Configuration: Boltz Rc | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 100% chirality percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: percentage of molecules with consistent chirality Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column chirality; footnote a |
| Configuration: Boltz R1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 0.406 protein_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column protein_rmsd; footnote a |
| Configuration: Boltz R1 | Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding Dataset subset: Plinder-L95 | 1.3 ligand_rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries Aggregation: median Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column ligand_rmsd; footnote a |
| 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 |
| Configuration: Boltz-1 | Task: Protein–ligand pose prediction Dataset: PLINDER-L95 | 1.39 Median ligand RMSD Å · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1: Protein–ligand pose prediction All entries; authors note this dataset contains structures seen during model training. Aggregation: Not reported Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column |
| Configuration: Boltz-2 | Task: Ligand potency prediction using generated poses Dataset: SARS-CoV-2 Mpro ligands | 0.8 Pearson R unitless · unknown Uncertainty: ± 0.027 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-2: Ligand potency prediction using generated poses Potency prediction using Boltz-2 ligand-pose generation protocol; see paper scoring pipeline. Aggregation: Not reported A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein–Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases · Table 3, Boltz-2 row, Pearson’s R column |
| Configuration: Boltz-1 | Task: Antibody–antigen interaction prediction using folded complexes Dataset: Antibody–antigen GEP test set | 0.85 AUC-ROC unitless · unknown Uncertainty: ± 0.05 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1: Antibody–antigen interaction prediction using folded complexes Interaction classifier evaluated using Boltz-1-folded input complexes; this is pipeline AUC, not DockQ. Aggregation: Not reported Enhancing antibody-antigen interaction prediction with atomic flexibility · Table 5, Folded row, Boltz-1 (no MSA) column |
| Configuration: Boltz-1 | Task: Protein–ligand pose prediction Dataset: Boltz-1 structure test set | 0.545 Top-1 ligand RMSD <2 Å rate unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-1: Protein–ligand pose prediction Highest-confidence pose from five samples; precomputed MSAs up to 4,096 sequences. Aggregation: Not reported Boltz-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. Release 2026-09-29-06401fd5b220.
Use this model
How it works, versions and access
Versions and evaluated configurations
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
Follow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied.
Stable record: discovery-model-boltzSpecifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-23. 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 count tied to the released structure, confidence and affinity checkpoints is not stated in the inspected report or model constructor. These components must be identified before comparing parameter totals. No total was inferred from file size or architecture names. · Not reported in inspected sourcesSources (2)Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction; jwohlwend/boltz: src/boltz/model/models/boltz2.py · XML sectionsS5-S12 Architecture and Training; src/boltz/model/models/boltz2.py Boltz2.__init__ component construction. |
| Known versions | Boltz-1 and Boltz-2 are separate model generations. In the Boltz-2 report, Boltz-2x means Boltz-2 with physicality steering potentials enabled; it is an inference condition, not evidence of a separately trained checkpoint.Sources (2)Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction; jwohlwend/boltz: README.md · README Introduction; XML sectionS15 paragraphP32 (Boltz-2x definition and Boltz-1 comparison). |
| Training data | Boltz-2 structure training uses experimental PDB structures released before 2023-06-01, MISATO/ATLAS/mdCATH molecular-dynamics ensembles, AlphaFold2 monomer predictions and Boltz-1 predictions of several complex types. Affinity regression uses filtered PubChem, ChEMBL and BindingDB assays; binary supervision uses PubChem HTS, CeMM and MIDAS plus synthetic decoys.SourcesBoltz-2: Towards Accurate and Efficient Binding Affinity Prediction · XML sectionS3 paragraphsP14-P16 Structural Data; sectionS4 paragraphsP20-P21 Binding Affinity Data. |
| Training cutoff | 2023-06-01 applies to release dates of experimental PDB structures used by Boltz-2. The source does not give a common cutoff for molecular dynamics, distilled predictions and affinity databases; this date must not be assigned to Boltz-1 or to all Boltz-2 training evidence.SourcesBoltz-2: Towards Accurate and Efficient Binding Affinity Prediction · XML P14 experimental PDB cutoff; P16 distillation and P20-P21 affinity sources. |
| Context limits | Boltz-2 training crops extend to 768 molecular tokens. This is a training setting, not a universal inference limit. Affinity training also crops predicted binding pockets; permitted input size depends on the actual inference implementation and resources.SourcesBoltz-2: Towards Accurate and Efficient Binding Affinity Prediction · XML sectionS6 paragraphP23 Trunk optimization; sectionS12 paragraphP29 Affinity training. |
| Weights licence | The official README explicitly releases all code and weights under MIT for academic and commercial use. This establishes distribution terms, not the identity of a checkpoint used by an external paper.Sourcesjwohlwend/boltz: README.md · README.md Introduction line19. |
| 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 | MIT for code at commit b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc.Sources (2)jwohlwend/boltz: LICENSE; jwohlwend/boltz: README.md · LICENSE MIT text; README.md Introduction line19. |
Applicable tests and references
Applicability is distinct from a completed evaluation.
- PLINDER · Proposed association
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
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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.
88 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | jwohlwend/boltz: docs/training.md 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | jwohlwend/boltz: docs/prediction.md 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | jwohlwend/boltz: src/boltz/model/models/boltz2.py 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | jwohlwend/boltz: scripts/train/configs/full.yaml 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: preprint; 1 | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | jwohlwend/boltz: README.md 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Diagram steps
| jwohlwend/boltz: docs/training.md 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Diagram steps
| jwohlwend/boltz: docs/prediction.md 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Diagram steps
| jwohlwend/boltz: src/boltz/model/models/boltz2.py 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Diagram steps
| jwohlwend/boltz: scripts/train/configs/full.yaml 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc | source checked automated source review · 2026-09-23 Audit detailsFollow-up review of Training data, Training cutoff, Context limits, Parameters, Code licence, Weights licence, Known versions. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: discovered
9 source records and release history
- jwohlwend/boltz official source · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- jwohlwend/boltz: README.md · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- jwohlwend/boltz: docs/prediction.md · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- jwohlwend/boltz: docs/training.md · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- jwohlwend/boltz: src/boltz/model/models/boltz2.py · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- jwohlwend/boltz: scripts/train/configs/full.yaml · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
- boltz2: Journal full-text XML · Original source · preprint; 1
- Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction · Original source · PMC full-text XML snapshot PMC12262699 at retrieval; byte-pinned by SHA-256
- jwohlwend/boltz: LICENSE · Original source · b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc
Technical metadata and extraction receipts
Stable ID: discovery-model-boltz
- areas
- molecular-interactions
- access
- official_source_linked
- benchmark applicability
- candidate; not evidence of a reported evaluation
- candidate benchmark ids
- discovery-benchmark-plinder
- entity level
- family
- reported name
- Boltz
- version
- Not reported
- historical missing metadata
- checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
- 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.
- entity classification
- review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-official-f780521ccebbb0691f9e; evidence-official-5a9e55abdf288d9dd8da; evidence-official-39a15ed8072aeea14a22; evidence-official-734117ed8501eb26fefc; evidence-official-7cb8cb7f091536b92c11; evidence-official-bd6ec1f819e22f075c32; source locator: 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; ambiguities: None recorded