Protocol

FoldBench protein-monomer published full-set assessment

Top-ranked of 25 predictions; OpenStructure v2.8, DockQ v2 for protein–nucleic-acid. Success: LRMSD <2 Å and LDDT-PLI >0.8 for ligand; DockQ ≥0.23 otherwise. Model-specific scored denominators retained.

5 evaluations · 20 results

Overview

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

5 recorded evaluations, 20 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

5 evaluations · 20 results. Different protocols are not a single leaderboard.

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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: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.92 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, GDT-TS row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.88 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, LDDT row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	1.95 rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, RMSD row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.94 tm-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, TM-score row, AlphaFold 3 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.91 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, GDT-TS row, Boltz-1 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.87 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, LDDT row, Boltz-1 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	1.97 rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, RMSD row, Boltz-1 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.94 tm-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, TM-score row, Boltz-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.9 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, GDT-TS row, Chai-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.87 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, LDDT row, Chai-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	2.1 rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, RMSD row, Chai-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.93 tm-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, TM-score row, Chai-1 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.91 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, GDT-TS row, HelixFold 3 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.86 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, LDDT row, HelixFold 3 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	2.03 rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, RMSD row, HelixFold 3 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.94 tm-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, TM-score row, HelixFold 3 column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.9 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, GDT-TS row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.86 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, LDDT row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	2.04 rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, RMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-monomer published full-set assessment Dataset: FoldBench protein-monomer published targets	0.93 tm-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-monomer block, TM-score row, Protenix column; Table 1 assessable count

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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Benchmarks

FoldBench

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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.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 5

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 2026-09-30-e37e3ab1284d. 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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Strengths, limitations and unresolved questions

Evidence

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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.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
Property and statement	Original source and location	Review and provenance
Relationship: part of ucc-research-benchmark-foldbench Individual claims	FoldBench official repository and evaluator Original source ↗ Supplementary Tables 1–3; Model Inference and Evaluation methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 4273f6877d82bd0b2fa476d1b2f34d121cbccc70 Retrieved: 2026-09-30T21:25:05Z	source checked automated source review · 2026-09-30T21:43:56Z Audit details Primary-source table transcription and scope review; no independent reproduction or human scientific review. Field: `links:part_of:ucc-research-benchmark-foldbench` Claim: ucc-research-membership-foldbench-protein-monomer Source artifact SHA-256: `Not recorded` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: part of ucc-research-benchmark-foldbench Individual claims	Benchmarking all-atom biomolecular structure prediction with FoldBench Original source ↗ Supplementary Tables 1–3; Model Inference and Evaluation methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41467-025-67127-3 Retrieved: 2026-09-30T21:23:29Z	source checked automated source review · 2026-09-30T21:43:56Z Audit details Primary-source table transcription and scope review; no independent reproduction or human scientific review. Field: `links:part_of:ucc-research-benchmark-foldbench` Claim: ucc-research-membership-foldbench-protein-monomer Source artifact SHA-256: `Not recorded` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: part of ucc-research-benchmark-foldbench Individual claims	FoldBench supplementary target coverage and performance Original source ↗ Supplementary Tables 1–3; Model Inference and Evaluation methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information to 10.1038/s41467-025-67127-3 Retrieved: 2026-09-30T21:26:52Z	source checked automated source review · 2026-09-30T21:43:56Z Audit details Primary-source table transcription and scope review; no independent reproduction or human scientific review. Field: `links:part_of:ucc-research-benchmark-foldbench` Claim: ucc-research-membership-foldbench-protein-monomer Source artifact SHA-256: `Not recorded` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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Release 2026-09-30-e37e3ab1284d · Record review: source checked

3 source records and release history

Benchmarking all-atom biomolecular structure prediction with FoldBench · Original source · 10.1038/s41467-025-67127-3
FoldBench supplementary target coverage and performance · Original source · Supplementary Information to 10.1038/s41467-025-67127-3
FoldBench official repository and evaluator · Original source · 4273f6877d82bd0b2fa476d1b2f34d121cbccc70

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Technical metadata and extraction receipts

Stable ID: ucc-research-protocol-foldbench-protein-monomer

review: method: automated_source_review; actor: Codex research coverage worker; reviewed at: 2026-09-30T21:43:56Z; note: Primary-source table transcription and scope review; no independent reproduction or human scientific review.
population limit: Compare with explicit model-specific assessable counts; do not claim matched scored population.
uncertainty: not reported in Table 3

Related records

dataset: FoldBench protein-monomer published targets
part of: FoldBench
protocol: foldbench protein monomer af3
protocol: foldbench protein monomer boltz1
protocol: foldbench protein monomer chai1
protocol: foldbench protein monomer helixfold3
protocol: foldbench protein monomer protenix
subject: Source membership: ucc-research-protocol-foldbench-protein-monomer

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