Configuration

Genie 3

Genie 3 generates protein designs through all-atom equivariant diffusion.

Sources (2)

aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table

1 evaluation · 5 metric rows

How it worksGenie 3 workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (2)

Overview

Model type

Diffusion-based protein backbone generator

Sources (2)

Inputs

Unconditional design specification, motif constraints or binder-design target context.

Sources (2)

Outputs

Sampled protein designs and outputs from the selected downstream evaluation workflow.

Sources (2)

Access

Official project documentation and implementation: https://github.com/aqlaboratory/genie3

Sources (2)

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

1 evaluation · 5 metric rows. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Genie 3	Protocol: Genie 3 short monomer generation designability: Unconditional short monomer Designability Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.97 designability reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Genie 3 on Genie 3 short monomer generation designability: Unconditional short monomer Designability Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 13 (Genie 3), column Designability
Configuration: Genie 3	Protocol: Genie 3 short monomer generation diversity-tm-05: Unconditional short monomer Diversity, TM < 0.5 Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.69 diversity_tm_05 reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Genie 3 on Genie 3 short monomer generation diversity-tm-05: Unconditional short monomer Diversity, TM < 0.5 Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 13 (Genie 3), column Diversity, TM < 0.5
Configuration: Genie 3	Protocol: Genie 3 short monomer generation diversity-tm-06: Unconditional short monomer Diversity, TM < 0.6 Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.85 diversity_tm_06 reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Genie 3 on Genie 3 short monomer generation diversity-tm-06: Unconditional short monomer Diversity, TM < 0.6 Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 13 (Genie 3), column Diversity, TM < 0.6
Configuration: Genie 3	Protocol: Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.36 novelty_afdb reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Genie 3 on Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 13 (Genie 3), column Novelty, AFDB
Configuration: Genie 3	Protocol: Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.37 novelty_pdb reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Genie 3 on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 13 (Genie 3), column Novelty, PDB

Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.

Use this model

How it works, versions and access

Related profile: Genie 3. This page retains the exact record and its evaluation context.

This configuration

Author-evaluated generation configuration; checkpoint/version and sampling parameters remain those described in Appendix B.2.

record: Genie 3
configuration: Not reported
entity type: Configuration

How it works

Genie 3 generates protein designs through all-atom equivariant diffusion. All-atom SE(3)-equivariant diffusion model, with separate generation and evaluation workflows. The documented inputs are unconditional design specification, motif constraints or binder-design target context. The output consists of sampled protein designs and outputs from the selected downstream evaluation workflow.

Sources (2)

Versions and reproducibility

Genie 3; repository includes compatibility guidance for Genie 2. The applicable input limits require configuration-specific checking.

Sources (2)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

One documented interface supports unconditional generation, motif scaffolding and binder design.
Sources (2)
aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table

Limitations and conditions

Genie 3 protein design is unrelated to GENIE3 gene-regulatory-network inference. A computationally generated design needs separate experimental validation.
Sources (2)
aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table

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-genie-3

Specifications

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.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Diffusion-based protein backbone generator Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Architecture	All-atom SE(3)-equivariant diffusion model, with separate generation and evaluation workflows. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Inputs	Unconditional design specification, motif constraints or binder-design target context. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Outputs	Sampled protein designs and outputs from the selected downstream evaluation workflow. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Parameters	The inspected release README and model card do not state a complete parameter total for the released all-atom diffusion checkpoint. · Not reported in inspected sources Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Known versions	Genie 3; repository includes compatibility guidance for Genie 2. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Training data	The released training manifests cover AlphaFoldDB representatives of at most 512 residues with pLDDT at least 70, and PiNDER 2024-02. These filters describe training components, not inference limits. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Training cutoff	The documented training inputs include PiNDER 2024-02 and filtered AlphaFoldDB representatives. This identifies a PiNDER release, not a universal latest-deposition cutoff for all training data. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Context limits	The README permits configured design-length ranges and distinguishes sampling settings above and below 300 residues; it does not state one validated maximum for all monomer, motif and binder tasks. · Not reported in inspected sources Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Weights licence	Apache-2.0 declared in the author-linked yeqinglin/genie3 model card. Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Access	Official project documentation and implementation: https://github.com/aqlaboratory/genie3 Sources (2) aqlaboratory/genie3: README.md; yeqinglin/genie3: README.md · README.md: overview, Download model weights and training data, Training and Codebase Architecture; author-linked yeqinglin/genie3 licence metadata; README.md: Training / Dataset manifest table
Code licence	Apache-2.0 Sources aqlaboratory/genie3: 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

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
Property and statement	Original source and location	Review and provenance
Relationship: family discovery-model-genie-3 Individual claims	Genie 3 primary paper v1, Table 3 Original source ↗ Appendix B.2–B.3; Table 3, row Genie 3 Version: 10.64898/2026.05.01.722168v1; posted 2026-05-05 Retrieved: 2026-09-23T11:22:04.377971+00:00	source checked automated source review · 2026-09-23 Audit details Source-backed evaluated identity only; no independent reproduction. Field: `links:family:discovery-model-genie-3` Claim: genie3-2026-table3-method-genie-3-discovery-model-genie-3-identity-claim Source artifact SHA-256: `43de8eab49ac74ad9141fbe955703a4e5f7879e0a83cbb547de37fc4e1d3e089` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-23-2b89723c6dd9 · Record review: source checked

1 source records and release history

Genie 3 primary paper v1, Table 3 · Original source · 10.64898/2026.05.01.722168v1; posted 2026-05-05

Download this release

Technical metadata and extraction receipts

Stable ID: genie3-2026-table3-method-genie-3

areas: proteins-complexes
source locator: Appendix B.2–B.3; Table 3, row Genie 3
missing metadata: checkpoint revision: unreported; parameters: unextracted

Related records

Suggest a correction