Boltz-1 (MSA) on ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
ESMFold2 Runs N’ Poses reported comparison evaluation of Boltz-1 (MSA) on Runs N’ Poses ligand pass rate (MSA), scored with Ligand pass rate.
Evaluation results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Evaluation procedure
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.
- 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)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- esmfold2-2026-runs-n-poses-task-msa
- metric implementation
- Ligand pass rate
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Ligand pass rate
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
16 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Author-evaluated co-folding using the named released model; no new fine-tuning inferred. Conditioning and inference budgets follow Figure 2C and Appendix A.2.10. Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Ligand pass rate Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id esmfold2-2026-runs-n-poses-task-msa Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.count_unit ligands Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evidence_overlap One receptor-ligand comparison reported at two conditioning modes and multiple inference settings; not independent benchmark replications. Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin author_reported Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.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. Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.published_score_reproduction false Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.scored_count 2573 Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 7 from left (Boltz-1 (MSA)), exact printed bar label Context-only references | 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 Version: 10.64898/2026.06.03.729735v1; posted 2026-06-04 | not individually reviewed No individual claim review recorded author reported Audit detailsField: 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-evaluation-boltz-1-msa-msa
- areas
- proteins-complexes
- tasks
- Runs N’ Poses ligand pass rate (MSA)
- origin
- author_reported
- 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.
- comparison
- protocol id: esmfold2-2026-runs-n-poses-task-msa; metric implementation: Ligand pass rate
- missing metadata
- uncertainty values: unextracted; eligible ligands: unreported
- source locator
- PDF page 5, Figure 2C, Runs N’ Poses subpanel (right), msa block, bar 7 from left (Boltz-1 (MSA)), exact printed bar label
- scored count
- 2573
- count unit
- ligands
- adaptation
- Author-evaluated co-folding using the named released model; no new fine-tuning inferred. Conditioning and inference budgets follow Figure 2C and Appendix A.2.10.
- evidence overlap
- One receptor-ligand comparison reported at two conditioning modes and multiple inference settings; not independent benchmark replications.
- published score reproduction
- false
- suite complete
- false
Related records
- benchmark: ESMFold2 Runs N’ Poses reported comparison msa: Runs N’ Poses ligand pass rate (MSA)
- model: Boltz-1 (MSA)
- dataset: Runs N’ Poses complete-case intersection: 2,573 scored ligands (ESMFold2 Runs N’ Poses reported comparison split)
- evaluation: Boltz-1 (MSA) · ESMFold2 Runs N’ Poses reported comparison msa · Ligand pass rate