Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB

Overview

Unconditional short monomer Novelty, AFDB. Scored with Novelty, AFDB 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

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Evaluation scope and datasetMetric and reported setup

Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB

novelty_afdb (reported score) · Higher values are better.

Every method Genie 3 short monomer generation reports on Unconditional short monomer Novelty, AFDB, scored with Novelty, AFDB on 500 generated monomers per run; lengths 50–250 in steps of 50; three runs.

Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB · 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, AFDB, PDF pages 18–20

Source-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.

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Tested configuration

0.220.2650.310.3550.4

Reported score

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Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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Benchmarks

Genie 3 unconditional short monomer comparison

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Recorded evaluations

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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.

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Author-reported evaluations: 13

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Null control

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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

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Evidence

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Evidence table

Inspect claims, sources and review details

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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: part of model-coverage-genie3-short-monomers Individual claims	Genie 3 primary paper v1, Table 3 Original source ↗ Appendix B.1–B.3; Table 3, column Novelty, AFDB, PDF pages 18–20 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 Primary-source transcription with no human sign-off and no independent reproduction. Field: `links:part_of:model-coverage-genie3-short-monomers` Claim: genie3-2026-table3-association-novelty-afdb Source artifact SHA-256: `43de8eab49ac74ad9141fbe955703a4e5f7879e0a83cbb547de37fc4e1d3e089` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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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

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Technical metadata and extraction receipts

Stable ID: genie3-2026-table3-task-novelty-afdb

areas: proteins-complexes
tasks: Unconditional short monomer Novelty, AFDB
metric: Novelty, AFDB
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, AFDB, PDF pages 18–20
comparison panels: id: genie3-2026-table3-panel-novelty-afdb; title: Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB; protocol id: genie3-2026-table3-task-novelty-afdb; dataset id: genie3-2026-table3-dataset-500-generated-monomers-per-run-lengths-50-250-in-steps-of-50-three-runs; metric: novelty_afdb; unit: reported score; direction: higher; result ids: genie3-2026-table3-result-rfdiffusion-novelty-afdb-novelty-afdb; genie3-2026-table3-result-frameflow-novelty-afdb-novelty-afdb; genie3-2026-table3-result-proteus-novelty-afdb-novelty-afdb; genie3-2026-table3-result-foldflow-2-base-novelty-afdb-novelty-afdb; genie3-2026-table3-result-foldflow-2-reft-novelty-afdb-novelty-afdb; genie3-2026-table3-result-proteina-mfs-novelty-afdb-novelty-afdb; genie3-2026-table3-result-la-proteina-ld1-novelty-afdb-novelty-afdb; genie3-2026-table3-result-la-proteina-ld2-novelty-afdb-novelty-afdb; genie3-2026-table3-result-protpardelle-1c-cc58-novelty-afdb-novelty-afdb; genie3-2026-table3-result-protpardelle-1c-cc94-novelty-afdb-novelty-afdb; genie3-2026-table3-result-genie-2-novelty-afdb-novelty-afdb; genie3-2026-table3-result-ambient-short-novelty-afdb-novelty-afdb; genie3-2026-table3-result-genie-3-novelty-afdb-novelty-afdb; source ids: model-coverage-genie3-2026-v1-source; source locator: Appendix B.1–B.3; Table 3, column Novelty, AFDB, PDF pages 18–20; context: Every method Genie 3 short monomer generation reports on Unconditional short monomer Novelty, AFDB, scored with Novelty, AFDB 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
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