Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 9 results. Different protocols are not a single leaderboard.
Protocol: FEP+ benchmark OpenFE subset, affinity ranking · Dataset: OpenFE subset of the public FEP benchmark
Sorted by Kendall tau (target average as printed, computed per assay and weighted by compound count) (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 | Kendall tau (target average as printed, computed per assay and weighted by compound count) | MAE (centered, computed per assay and averaged across assays weighted by compound count) | MAE (non-centered, computed per assay and averaged across assays weighted by compound count) | MAE (pairwise, target average as printed, computed per assay and weighted by compound count) | Pearson (target average as printed, computed per assay and weighted by compound count) | Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) | Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) | Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) | Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) |
|---|---|---|---|---|---|---|---|---|---|
| Boltz-2 ipTM as an affinity scoreEvaluation | -0.05 | N/A | N/A | N/A | -0.07 | N/A | N/A | N/A | N/A |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | -0.05 Kendall tau (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "Kendall tau", sub-column "target avg." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A MAE (centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "MAE", sub-column "cent." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A MAE (non-centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "MAE", sub-column "non-cent." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | -0.07 Pearson (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "Pearson R", sub-column "target avg." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A MAE (pairwise, target average as printed, computed per assay and weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "PMAE", sub-column "target avg." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "Perc. within 1", sub-column "cent." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "Perc. within 1", sub-column "non-cent." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "Perc. within 2", sub-column "cent." (text-layer line 1691) |
| Configuration: Boltz-2 ipTM as an affinity score | Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark | N/A Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBoltz-2 iptm on the FEP+ benchmark OpenFE subset uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 11, row "Boltz-2 iptm", column "Perc. within 2", sub-column "non-cent." (text-layer line 1691) |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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FEP+ benchmark OpenFE subset, affinity ranking
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Published model applied without retraining; the interface confidence is read in place of an affinity Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: aggregation Calculated per assay and averaged across assays with weight proportional to the number of compounds in each assay (appendix D.2.2, 'Evaluation metrics'). The Pearson R, Kendall tau and PMAE columns are printed under the label 'target avg.'; assays and targets are not the same unit, and the source does not reconcile the printed label with the stated computation. Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: budget Not reported Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: dataset version the FEP+ benchmark OpenFE subset Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: inputs Protein sequence and ligand structure Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: metric implementation Appendix D.2.2 'Evaluation metrics': Pearson R, Kendall tau, pairwise MAE (PMAE), MAE and the fraction of predictions within 1 and 2 kcal/mol, each computed per assay and averaged across assays weighted by compound count, with predictions converted to kcal/mol first; the centered variants translate each assay's predictions to the ground-truth mean Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: population 876 protein-ligand complexes Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: protocol id uc-leadopt-20261022-protocol-boltz2-fep-openfe-subset Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Comparison: split Held-out affinity test set Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Origin author_reported Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 11, row 'Boltz-2 iptm' (text-layer line 1691) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: uc-leadopt-20261022-eval-t11-boltz-2-iptm