Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split)
Dataset subset reported in ESMFold2 primary paper v1, Figure 2C Runs N’ Poses. Exact split manifest remains unextracted; source-table identity is retained.
Evaluation results
11 evaluations · 11 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaFold3 (MSA) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 69% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 8 from left (AlphaFold3 (MSA)), exact printed bar label |
| Configuration: Boltz-1 (MSA) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 60% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 7 from left (Boltz-1 (MSA)), exact printed bar label |
| Configuration: Chai-1 (MSA) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 59% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceChai-1 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 5 from left (Chai-1 (MSA)), exact printed bar label |
| Configuration: Chai-1 (single sequence) | Protocol: ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 51% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), single-sequence block, bar 1 from left (Chai-1 (single sequence)), exact printed bar label |
| Configuration: ESMFold2-Fast (single sequence) | Protocol: ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 65% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), single-sequence block, bar 2 from left (ESMFold2-Fast (single sequence)), exact printed bar label |
| Configuration: ESMFold2 (MSA, 10 loops) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 67% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 10 from left (ESMFold2 (MSA, 10 loops)), exact printed bar label |
| Configuration: ESMFold2 (MSA, 20 loops) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 68% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 11 from left (ESMFold2 (MSA, 20 loops)), exact printed bar label |
| Configuration: ESMFold2 (single sequence, 10 loops) | Protocol: ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 66% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), single-sequence block, bar 3 from left (ESMFold2 (single sequence, 10 loops)), exact printed bar label |
| Configuration: ESMFold2 (single sequence, 20 loops) | Protocol: ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 66% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), single-sequence block, bar 4 from left (ESMFold2 (single sequence, 20 loops)), exact printed bar label |
| Configuration: OpenFold3 (MSA) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 60% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 6 from left (OpenFold3 (MSA)), exact printed bar label |
| Configuration: Protenix-v1 (MSA) | Protocol: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA) Dataset subset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) | 66% ligand_pass_rate percent · higher Uncertainty: Not reported Coverage: unit: ligands; scored: 2573; eligible: unreported; note: Complete-case intersection; source 2600 systems is not a ligand denominator. | Author-reported evaluation · source checkedMethods, coverage and sourceRuns 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. Aggregation: Not reported ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 9 from left (Protenix-v1 (MSA)), exact printed bar label |
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Subset and evaluation context
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Evidence
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Evidence table
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description Dataset subset reported in ESMFold2 primary paper v1, Figure 2C Runs N’ Poses. Exact split manifest remains unextracted; source-table identity is retained. Context-only references | ESMFold2 primary paper v1, Figure 2C Runs N’ Poses No field-specific location recorded Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split) Context-only references | ESMFold2 primary paper v1, Figure 2C Runs N’ Poses No field-specific location recorded Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
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- ESMFold2 primary paper v1, Figure 2C Runs N’ Poses · Original source · 10.64898/2026.06.03.729735v1; posted 2026-06-04
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Stable ID: esmfold2-2026-runs-n-poses-dataset-runs-n-poses-complete-case-intersection-2-573-scored-ligands
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Related records
- dataset: AlphaFold3 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- dataset: Boltz-1 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- dataset: Chai-1 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- dataset: Chai-1 (single sequence) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- dataset: ESMFold2-Fast (single sequence) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- dataset: ESMFold2 (MSA, 10 loops) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- dataset: ESMFold2 (MSA, 20 loops) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- dataset: ESMFold2 (single sequence, 10 loops) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- dataset: ESMFold2 (single sequence, 20 loops) on ESMFold2 Runs N’ Poses reported comparison single-sequence: Runs N’ Poses ligand pass rate (single sequence)
- dataset: OpenFold3 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- dataset: Protenix-v1 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)