ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
Runs N’ Poses ligand pass rate (single sequence). Scored with Ligand pass rate on Runs N’ Poses complete-case intersection: 2,573 scored ligands. Runs N’ Poses receptor–ligand co-folding; source benchmark 2,600 systems. Figure 2C reports n=2,573 scored ligands on the intersection where all models produced valid predictions, after excluding undefined SuCOS scores. Multiple ligands in one system are scored independently. Five seeds × five diffusion samples per target; select top candidate by ipTM. Success requires lDDT-PLI >0.8 and BiSyRMSD <2 angstrom. Baselines use 10 recycles and 200 diffusion steps; ESMFold2 uses 10 or 20 loops as labelled and truncated 68-step diffusion. Single-sequence and MSA conditions remain separate.
Overview
Runs N’ Poses ligand pass rate (single sequence). Scored with Ligand pass rate on Runs N’ Poses complete-case intersection: 2,573 scored ligands. Runs N’ Poses receptor–ligand co-folding; source benchmark 2,600 systems. Figure 2C reports n=2,573 scored ligands on the intersection where all models produced valid predictions, after excluding undefined SuCOS scores. Multiple ligands in one system are scored independently. Five seeds × five diffusion samples per target; select top candidate by ipTM. Success requires lDDT-PLI >0.8 and BiSyRMSD <2 angstrom. Baselines use 10 recycles and 200 diffusion steps; ESMFold2 uses 10 or 20 loops as labelled and truncated 68-step diffusion. Single-sequence and MSA conditions remain separate.
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.
ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
ligand_pass_rate (percent) · Higher values are better.
Every method ESMFold2 Runs N’ Poses reported comparison reports on Runs N’ Poses ligand pass rate (single sequence), scored with Ligand pass rate on Runs N’ Poses complete-case intersection: 2,573 scored ligands.
ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence) · Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · Figure 2C right subpanel; Appendix A.2.10 Runs N’ Poses, PDF pages 5, 46–47Author-reported integer-rounded labels from the original figure, not raw unrounded scores or independent reproductions. All 11 labelled bars in this subpanel are retained.
All comparison limitations (5)
- Author-reported integer-rounded labels from the original figure, not raw unrounded scores or independent reproductions. All 11 labelled bars in this subpanel are retained.
- The two panels separate single-sequence and MSA conditioning. Loop counts, inference settings and model versions remain in configuration labels.
- n=2,573 counts scored ligands, not independent receptor systems. Results use the source’s complete-case intersection and omit ligands without defined SuCOS scores.
- The source shows graphical ±1 sigma uncertainty from 200 bootstrap resamples. Exact error-bar values are not printed in this subpanel and remain unextracted; no numerical uncertainty was estimated.
- The general OpenFold family record describes OpenFold/AlphaFold2; this OpenFold3 baseline receives no unsupported family link. Protenix-v1 also remains an independently named baseline.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 4 of 4 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.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Chai-1 (single sequence) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- ESMFold2-Fast (single sequence) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- ESMFold2 (single sequence, 10 loops) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- ESMFold2 (single sequence, 20 loops) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
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
- 4
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-esmfold2-runs-n-poses Individual claims | ESMFold2 primary paper v1, Figure 2C Runs N’ Poses Figure 2C right subpanel; Appendix A.2.10 Runs N’ Poses, PDF pages 5, 46–47 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | source checked automated source review · 2026-09-23 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: esmfold2-2026-runs-n-poses-association-single-sequence 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
- ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · Original source · 10.64898/2026.06.03.729735v1; posted 2026-06-04
Technical metadata and extraction receipts
Stable ID: esmfold2-2026-runs-n-poses-task-single-sequence
- areas
- proteins-complexes
- tasks
- Runs N’ Poses ligand pass rate (single sequence)
- metric
- Ligand pass rate
- metric direction
- higher
- dataset
- Runs N’ Poses complete-case intersection: 2,573 scored ligands
- protocol
- Runs N’ Poses receptor–ligand co-folding; source benchmark 2,600 systems. Figure 2C reports n=2,573 scored ligands on the intersection where all models produced valid predictions, after excluding undefined SuCOS scores. Multiple ligands in one system are scored independently. Five seeds × five diffusion samples per target; select top candidate by ipTM. Success requires lDDT-PLI >0.8 and BiSyRMSD <2 angstrom. Baselines use 10 recycles and 200 diffusion steps; ESMFold2 uses 10 or 20 loops as labelled and truncated 68-step diffusion. Single-sequence and MSA conditions remain separate.
- source locator
- Figure 2C right subpanel; Appendix A.2.10 Runs N’ Poses, PDF pages 5, 46–47
- comparison panels
- id: esmfold2-2026-runs-n-poses-panel-single-sequence; title: ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence); protocol id: esmfold2-2026-runs-n-poses-task-single-sequence; dataset id: esmfold2-2026-runs-n-poses-dataset-runs-n-poses-complete-case-intersection-2-573-scored-ligands; metric: ligand_pass_rate; unit: percent; direction: higher; result ids: esmfold2-2026-runs-n-poses-result-chai-1-single-sequence-single-sequence-ligand-pass-rate; esmfold2-2026-runs-n-poses-result-esmfold2-fast-single-sequence-single-sequence-ligand-pass-rate; esmfold2-2026-runs-n-poses-result-esmfold2-single-sequence-10-loops-single-sequence-ligand-pass-rate; esmfold2-2026-runs-n-poses-result-esmfold2-single-sequence-20-loops-single-sequence-ligand-pass-rate; source ids: model-coverage-esmfold2-2026-v1-source; source locator: Figure 2C right subpanel; Appendix A.2.10 Runs N’ Poses, PDF pages 5, 46–47; context: Every method ESMFold2 Runs N’ Poses reported comparison reports on Runs N’ Poses ligand pass rate (single sequence), scored with Ligand pass rate on Runs N’ Poses complete-case intersection: 2,573 scored ligands.; caveats: Author-reported integer-rounded labels from the original figure, not raw unrounded scores or independent reproductions. All 11 labelled bars in this subpanel are retained.; The two panels separate single-sequence and MSA conditioning. Loop counts, inference settings and model versions remain in configuration labels.; n=2,573 counts scored ligands, not independent receptor systems. Results use the source’s complete-case intersection and omit ligands without defined SuCOS scores.; The source shows graphical ±1 sigma uncertainty from 200 bootstrap resamples. Exact error-bar values are not printed in this subpanel and remain unextracted; no numerical uncertainty was estimated.; The general OpenFold family record describes OpenFold/AlphaFold2; this OpenFold3 baseline receives no unsupported family link. Protenix-v1 also remains an independently named baseline.; review: method: automated_source_review; date: 2026-09-23
- entity level
- protocol
Related records
- part of: ESMFold2 Runs N’ Poses comparison
- subject: ESMFold2 Runs N’ Poses reported comparison single-sequence: part of model-coverage-esmfold2-runs-n-poses
- benchmark: Chai-1 (single sequence) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- benchmark: ESMFold2-Fast (single sequence) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- benchmark: ESMFold2 (single sequence, 10 loops) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- benchmark: ESMFold2 (single sequence, 20 loops) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)