Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
Unconditional short monomer Novelty, PDB. Scored with Novelty, PDB on 500 generated monomers per run; lengths 50–250 in steps of 50; three runs. 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.
Overview
Unconditional short monomer Novelty, PDB. Scored with Novelty, PDB on 500 generated monomers per run; lengths 50–250 in steps of 50; three runs. 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.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
novelty_pdb (reported score) · Higher values are better.
Every method Genie 3 short monomer generation reports on Unconditional short monomer Novelty, PDB, scored with Novelty, PDB on 500 generated monomers per run; lengths 50–250 in steps of 50; three runs.
Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB · 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
Genie 3 primary paper v1, Table 3 · Appendix B.1–B.3; Table 3, column Novelty, PDB, PDF pages 18–20Source-checked author-reported results, not independently reproduced. All 13 method/version rows are retained.
All comparison limitations (6)
- Source-checked author-reported results, not independently reproduced. All 13 method/version rows are retained.
- The five metrics are separate; no cross-metric aggregate is defined. Original fractional-scale printed values are preserved without rescaling.
- Table 3 reports averages across three runs, not confidence intervals. Per-run tables 4 and 5 are retained in the source but are not extra independent evidence.
- Diversity is reported on the table’s fractional scale; Appendix B.1 describes cluster counts but does not explicitly state the displayed normalization. Exact original values are preserved.
- Novelty is mean one minus maximum structural similarity among designable structures; unmatched exhaustive-search cases receive novelty 1 in the source procedure.
- The alpha/beta secondary-structure percentages are retained in the 91-cell source receipt as descriptive metadata and excluded from directional rankings.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 12 of 13 matching rows.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Ambient (short) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- FoldFlow 2 (base) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- FoldFlow 2 (reft) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- FrameFlow on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- Genie 2 on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- Genie 3 on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- La-Proteina (LD1) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- La-Proteina (LD2) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- Proteina (MFS) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- Proteus on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- Protpardelle-1c (cc58) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- Protpardelle-1c (cc94) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 13
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Protocol-specific valid geometric or structural control
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Upstream conventional structural reference with matched templates and cutoffs
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
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: part of model-coverage-genie3-short-monomers Individual claims | Genie 3 primary paper v1, Table 3 Appendix B.1–B.3; Table 3, column Novelty, PDB, PDF pages 18–20 Version: 10.64898/2026.05.01.722168v1; posted 2026-05-05 | source checked automated source review · 2026-09-23 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: genie3-2026-table3-association-novelty-pdb Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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
Technical metadata and extraction receipts
Stable ID: genie3-2026-table3-task-novelty-pdb
- areas
- proteins-complexes
- tasks
- Unconditional short monomer Novelty, PDB
- metric
- Novelty, PDB
- metric direction
- higher
- dataset
- 500 generated monomers per run; lengths 50–250 in steps of 50; three runs
- protocol
- 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.
- source locator
- Appendix B.1–B.3; Table 3, column Novelty, PDB, PDF pages 18–20
- comparison panels
- id: genie3-2026-table3-panel-novelty-pdb; title: Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB; protocol id: genie3-2026-table3-task-novelty-pdb; dataset id: genie3-2026-table3-dataset-500-generated-monomers-per-run-lengths-50-250-in-steps-of-50-three-runs; metric: novelty_pdb; unit: reported score; direction: higher; result ids: genie3-2026-table3-result-rfdiffusion-novelty-pdb-novelty-pdb; genie3-2026-table3-result-frameflow-novelty-pdb-novelty-pdb; genie3-2026-table3-result-proteus-novelty-pdb-novelty-pdb; genie3-2026-table3-result-foldflow-2-base-novelty-pdb-novelty-pdb; genie3-2026-table3-result-foldflow-2-reft-novelty-pdb-novelty-pdb; genie3-2026-table3-result-proteina-mfs-novelty-pdb-novelty-pdb; genie3-2026-table3-result-la-proteina-ld1-novelty-pdb-novelty-pdb; genie3-2026-table3-result-la-proteina-ld2-novelty-pdb-novelty-pdb; genie3-2026-table3-result-protpardelle-1c-cc58-novelty-pdb-novelty-pdb; genie3-2026-table3-result-protpardelle-1c-cc94-novelty-pdb-novelty-pdb; genie3-2026-table3-result-genie-2-novelty-pdb-novelty-pdb; genie3-2026-table3-result-ambient-short-novelty-pdb-novelty-pdb; genie3-2026-table3-result-genie-3-novelty-pdb-novelty-pdb; source ids: model-coverage-genie3-2026-v1-source; source locator: Appendix B.1–B.3; Table 3, column Novelty, PDB, PDF pages 18–20; context: Every method Genie 3 short monomer generation reports on Unconditional short monomer Novelty, PDB, scored with Novelty, PDB on 500 generated monomers per run; lengths 50–250 in steps of 50; three runs.; caveats: Source-checked author-reported results, not independently reproduced. All 13 method/version rows are retained.; The five metrics are separate; no cross-metric aggregate is defined. Original fractional-scale printed values are preserved without rescaling.; Table 3 reports averages across three runs, not confidence intervals. Per-run tables 4 and 5 are retained in the source but are not extra independent evidence.; Diversity is reported on the table’s fractional scale; Appendix B.1 describes cluster counts but does not explicitly state the displayed normalization. Exact original values are preserved.; Novelty is mean one minus maximum structural similarity among designable structures; unmatched exhaustive-search cases receive novelty 1 in the source procedure.; The alpha/beta secondary-structure percentages are retained in the 91-cell source receipt as descriptive metadata and excluded from directional rankings.; review: method: automated_source_review; date: 2026-09-23
- entity level
- protocol
Related records
- part of: Genie 3 unconditional short monomer comparison
- subject: Genie 3 short monomer generation novelty-pdb: part of model-coverage-genie3-short-monomers
- benchmark: Ambient (short) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: FoldFlow 2 (base) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: FoldFlow 2 (reft) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: FrameFlow on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: Genie 2 on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: Genie 3 on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: La-Proteina (LD1) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: La-Proteina (LD2) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: Proteina (MFS) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: Proteus on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: Protpardelle-1c (cc58) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: Protpardelle-1c (cc94) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB
- benchmark: RFDiffusion on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB