Configuration

Protenix — FoldBench published inference

5 seeds × 5 samples, 10 recycles; highest model ranking score. Paper-specific input/code adjustments; H800 80GB inference.

9 evaluations · 35 results

Overview

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

Evaluations and results

9 evaluations · 35 results. Different protocols are not a single leaderboard.

Sorted by lDDT (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	lDDT	FoldBench success rate	CAPRI interface RMSD	CAPRI ligand RMSD	GDT ts	RMSD	TM score	lDDT-LP	lDDT-PLI
Protenix — FoldBench published inferenceEvaluation	FoldBench protein-monomer published full-set assessment, FoldBench protein-monomer published targets	0.86 (best in column)	Not reported	Not reported	Not reported	0.9 (best in column)	2.04 (best in column)	0.93 (best in column)	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench antibody-antigen published full-set assessment, FoldBench antibody-antigen published targets	0.85	34.1%	8.91	30.4	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench protein-dna published full-set assessment, FoldBench protein-dna published targets	0.83	68.4%	5.08	11.6	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench protein-peptide published full-set assessment, FoldBench protein-peptide published targets	0.83	77.1% (best in column)	2.93 (best in column)	8.44 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench protein-protein published full-set assessment, FoldBench protein-protein published targets	0.81	68.2%	7.22	17.5	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench protein-rna published full-set assessment, FoldBench protein-rna published targets	0.75	44.8%	8.88	22.3	Not reported	Not reported	Not reported	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench rna-monomer published full-set assessment, FoldBench rna-monomer published targets	0.59	Not reported	Not reported	Not reported	0.55	9.24	0.38	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench dna-monomer published full-set assessment, FoldBench dna-monomer published targets	0.44	Not reported	Not reported	Not reported	0.52	7.4	0.28	Not reported	Not reported
Protenix — FoldBench published inferenceEvaluation	FoldBench protein-ligand published full-set assessment, FoldBench protein-ligand published targets	Not reported	50.7%	Not reported	Not reported	Not reported	Not reported	Not reported	0.89	0.7

All 35 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	8.91 CAPRI interface RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, iRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	0.85 lDDT fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, LDDT row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	30.4 CAPRI ligand RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, lRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	34.1% FoldBench success rate percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, Success rate row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.52 GDT ts fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, GDT-TS row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.44 lDDT fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, LDDT row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	7.4 RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, RMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.28 TM score unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, TM-score row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-dna published full-set assessment Dataset: FoldBench protein-dna published targets	5.08 CAPRI interface RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein dna protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-dna block, iRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-dna published full-set assessment Dataset: FoldBench protein-dna published targets	0.83 lDDT fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein dna protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-dna block, LDDT row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-dna published full-set assessment Dataset: FoldBench protein-dna published targets	11.6 CAPRI ligand RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein dna protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-dna block, lRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-dna published full-set assessment Dataset: FoldBench protein-dna published targets	68.4% FoldBench success rate percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein dna protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-dna block, Success rate row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-ligand published full-set assessment Dataset: FoldBench protein-ligand published targets	0.89 lDDT-LP fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein ligand protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-ligand block, LDDT-LP row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-ligand published full-set assessment Dataset: FoldBench protein-ligand published targets	0.7 lDDT-PLI fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein ligand protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-ligand block, LDDT-PLI row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-ligand published full-set assessment Dataset: FoldBench protein-ligand published targets	50.7% FoldBench success rate percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein ligand protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-ligand block, Success rate 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	0.9 GDT ts fraction · higher Uncertainty: Not yet extracted 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 yet extracted 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 yet extracted 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 unitless · higher Uncertainty: Not yet extracted 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
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-peptide published full-set assessment Dataset: FoldBench protein-peptide published targets	2.93 CAPRI interface RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein peptide protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-peptide block, iRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-peptide published full-set assessment Dataset: FoldBench protein-peptide published targets	0.83 lDDT fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein peptide protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-peptide block, LDDT row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-peptide published full-set assessment Dataset: FoldBench protein-peptide published targets	8.44 CAPRI ligand RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein peptide protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-peptide block, lRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-peptide published full-set assessment Dataset: FoldBench protein-peptide published targets	77.1% FoldBench success rate percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein peptide protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-peptide block, Success rate row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-protein published full-set assessment Dataset: FoldBench protein-protein published targets	7.22 CAPRI interface RMSD angstrom · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein protein protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-protein block, iRMSD row, Protenix column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench protein-protein published full-set assessment Dataset: FoldBench protein-protein published targets	0.81 lDDT fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench protein protein protenix Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, protein-protein block, LDDT row, Protenix column; Table 1 assessable count

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Evidence

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Evidence table

Inspect claims, sources and review details

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2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Facets: method types 1 values foundation_model Individual claims	Benchmarking all-atom biomolecular structure prediction with FoldBench Original source ↗ Matches other AlphaFold 3 and Chai-1 configurations 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	conflicting claim ["automated-source-review"] · 2026-10-12 Audit details Correct the method type from none to foundation_model (use-case baseline review 2026-10-12, table 2). The review did not read FoldBench. Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"foundation_model\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-736ffa8de7e4bcb7cd58 Source artifact SHA-256: `3104bc7a0c5dd138421edfae72008fe1369b18192702fb7474a2517aece31928` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Facets: method types 1 values foundation_model Individual claims	FoldBench supplementary target coverage and performance Original source ↗ Matches other AlphaFold 3 and Chai-1 configurations 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	conflicting claim ["automated-source-review"] · 2026-10-12 Audit details Correct the method type from none to foundation_model (use-case baseline review 2026-10-12, table 2). The review did not read FoldBench. Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"foundation_model\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-736ffa8de7e4bcb7cd58 Source artifact SHA-256: `c699bd6b7ef8277ce4f89d12ff2365cd7a199dbc7eb4b674aeba4e62da92d5bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

2 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

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Technical metadata and extraction receipts

Stable ID: ucc-research-config-foldbench-protenix

method types: foundation_model
review: method: automated-source-review; reviewed at: 2026-09-30T21:43:56Z; note: Primary-source table transcription and scope review; no independent reproduction or human scientific review.; reviewer note: role: research coverage worker; reviewer: codex
code commit: ca0170c256cc1e39ac2b4f330401a6419f0e97f3
samples: 25
recycles: 10
selection: highest model ranking score
missing metadata: weights sha256: reason: unextracted

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