FoldBench | benchmark

Overview

Source study/challenge grouping of the exact imported protocols. No claim that this intake implements or reproduces an executable benchmark.

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

45 recorded evaluations, 175 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

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

All evaluations

45 evaluations · 175 results. 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: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	7.4 irmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, iRMSD row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen 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 antibody antigen af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, LDDT row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	24.5 lrmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, lRMSD row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	47.9% success-rate percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, Success rate row, AlphaFold 3 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	8.8 irmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, iRMSD row, Boltz-1 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	0.84 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, LDDT row, Boltz-1 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	30.7 lrmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, lRMSD row, Boltz-1 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	33.5% success-rate percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, Success rate row, Boltz-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	10.5 irmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, iRMSD row, Chai-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	0.85 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, LDDT row, Chai-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	33.4 lrmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, lRMSD row, Chai-1 column; Table 1 assessable count
Configuration: Chai-1 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	23.6% success-rate percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen chai1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, Success rate row, Chai-1 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	9.97 irmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, iRMSD row, HelixFold 3 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	0.84 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, LDDT row, HelixFold 3 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	33 lrmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, lRMSD row, HelixFold 3 column; Table 1 assessable count
Configuration: HelixFold 3 — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	28.4% success-rate percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench antibody antigen helixfold3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, antibody-antigen block, Success rate row, HelixFold 3 column; Table 1 assessable count
Configuration: Protenix — FoldBench published inference	Protocol: FoldBench antibody-antigen published full-set assessment Dataset: FoldBench antibody-antigen published targets	8.91 irmsd angstrom · lower Uncertainty: Not reported 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 reported 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 lrmsd angstrom · lower Uncertainty: Not reported 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% success-rate percent · higher Uncertainty: Not reported 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: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.58 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, GDT-TS row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.53 lddt fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, LDDT row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	6.48 rmsd angstrom · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, RMSD row, AlphaFold 3 column; Table 1 assessable count
Configuration: AlphaFold 3 — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.31 tm-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer af3 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, TM-score row, AlphaFold 3 column; Table 1 assessable count
Configuration: Boltz-1 — FoldBench published inference	Protocol: FoldBench dna-monomer published full-set assessment Dataset: FoldBench dna-monomer published targets	0.55 gdt-ts fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source foldbench dna monomer boltz1 Not reported Aggregation: source table mean FoldBench supplementary target coverage and performance · Supplementary Table 3, dna-monomer block, GDT-TS row, Boltz-1 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

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Protocols

These source-backed links do not make different protocols or scores interchangeable.

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 18 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

Baseline status by linked protocol

FoldBench antibody-antigen published full-set assessment · 0/2 roles measured
FoldBench dna-monomer published full-set assessment · 0/2 roles measured
FoldBench protein-dna published full-set assessment · 0/2 roles measured
FoldBench protein-ligand published full-set assessment · 0/2 roles measured
FoldBench protein-monomer published full-set assessment · 0/2 roles measured
FoldBench protein-peptide published full-set assessment · 0/2 roles measured
FoldBench protein-protein published full-set assessment · 0/2 roles measured
FoldBench protein-rna published full-set assessment · 0/2 roles measured
FoldBench rna-monomer published full-set assessment · 0/2 roles measured

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 this benchmark

Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.

Run instructions

No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
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Sources and history

View linked audit checks and correction history

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-benchmark-foldbench

entity level: suite
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.
source locator: Supplementary Tables 1–3; Model Inference and Evaluation methods

Related records

part of: FoldBench antibody-antigen published full-set assessment
part of: FoldBench dna-monomer published full-set assessment
part of: FoldBench protein-dna published full-set assessment
part of: FoldBench protein-ligand published full-set assessment
part of: FoldBench protein-monomer published full-set assessment
part of: FoldBench protein-peptide published full-set assessment
part of: FoldBench protein-protein published full-set assessment
part of: FoldBench protein-rna published full-set assessment
part of: FoldBench rna-monomer published full-set assessment