Dataset

Four-target subset of the public FEP benchmark

87 neutral compounds against CDK2, TYK2, JNK1 and P38 with measured affinities.

Evaluation results

10 evaluations · 100 results. Different protocols are not a single leaderboard.

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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: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.54 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "Kendall tau", sub-column "target avg." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.65 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "MAE", sub-column "cent." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	2.47 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "MAE", sub-column "non-cent." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.75 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "Pearson R", sub-column "target avg." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.95 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "PMAE", sub-column "target avg." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	>20 GPU hours Accelerator time (per-method cost as printed beside the accuracy columns) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "time" (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.79 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "Perc. within 1", sub-column "cent." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.11 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "Perc. within 1", sub-column "non-cent." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.98 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "Perc. within 2", sub-column "cent." (text-layer line 1712)
Configuration: ABFE protocol optimised on the four-target subset	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.4 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	Evaluation origin not reported · Source checked Methods, coverage and source ABFE on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "ABFE", column "Perc. within 2", sub-column "non-cent." (text-layer line 1712)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.09 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "Kendall tau", sub-column "target avg." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.82 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "MAE", sub-column "cent." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	1.4 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "MAE", sub-column "non-cent." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.14 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "Pearson R", sub-column "target avg." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	1.18 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "PMAE", sub-column "target avg." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.48 GPU ms Accelerator time (per-method cost as printed beside the accuracy columns) millisecond · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "time" (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.62 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "Perc. within 1", sub-column "cent." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.43 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "Perc. within 1", sub-column "non-cent." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	1 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "Perc. within 2", sub-column "cent." (text-layer line 1708)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.73 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 checked Methods, coverage and source BACPI on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "BACPI", column "Perc. within 2", sub-column "non-cent." (text-layer line 1708)
Configuration: Boltz-2 ipTM as an affinity score	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.09 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 checked Methods, coverage and source Boltz-2 iptm on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2 iptm", column "Kendall tau", sub-column "target avg." (text-layer line 1707)
Configuration: Boltz-2 ipTM as an affinity score	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target 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 checked Methods, coverage and source Boltz-2 iptm on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2 iptm", column "MAE", sub-column "cent." (text-layer line 1707)
Configuration: Boltz-2 ipTM as an affinity score	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target 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 checked Methods, coverage and source Boltz-2 iptm on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2 iptm", column "MAE", sub-column "non-cent." (text-layer line 1707)
Configuration: Boltz-2 ipTM as an affinity score	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.04 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 checked Methods, coverage and source Boltz-2 iptm on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2 iptm", column "Pearson R", sub-column "target avg." (text-layer line 1707)
Configuration: Boltz-2 ipTM as an affinity score	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target 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 checked Methods, coverage and source Boltz-2 iptm on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "Boltz-2 iptm", column "PMAE", sub-column "target avg." (text-layer line 1707)

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

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Verified: Not verified

Evidence incomplete

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Verified: Not verified

Evidence incomplete

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Verified: Not verified

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Missing or unresolved evidence

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Dataset and evaluation context

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Evidence

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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.

7 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Population 87 neutral compounds over 4 targets (CDK2, TYK2, JNK1, P38) Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact
Scope note The supplement attributes the 87 compounds to 'Chen et al., 2023'. The citation does not resolve to a congeneric-series paper in the reference list, so the series definition behind this subset is not established. Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.scope_note` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact
Source location Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact
Split Held-out affinity test set Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact
Version Subset of the FEP+ benchmark as used in the Boltz-2 supplement; ligand sets curated in the protein-ligand-benchmark of Hahn et al. 2022 Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact
Description 87 neutral compounds against CDK2, TYK2, JNK1 and P38 with measured affinities. Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact
Name Four-target subset of the public FEP benchmark Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]' Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) Retrieved: 2026-10-22T11:52:00Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569` 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 Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Original source · bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344)

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Stable ID: uc-leadopt-20261022-data-fep-4target

areas: molecular-interactions
contexts: research
version: Subset of the FEP+ benchmark as used in the Boltz-2 supplement; ligand sets curated in the protein-ligand-benchmark of Hahn et al. 2022
split: Held-out affinity test set
population: 87 neutral compounds over 4 targets (CDK2, TYK2, JNK1, P38)
source locator: Appendix D.2.1, 'a 4 targets subset (CDK2, TYK2, JNK1, P38; curated in the protein-ligand-benchmark [Hahn et al., 2022]) with 87 neutral compounds [Chen et al., 2023]'
scope note: The supplement attributes the 87 compounds to 'Chen et al., 2023'. The citation does not resolve to a congeneric-series paper in the reference list, so the series definition behind this subset is not established.
review: method: source-hash-verification; pdf-text-parse; independent-cell-check; rendered-source-visual-check; ai-assisted-source-review; method note: Re-retrieved all three sources and matched each pinned SHA-256. Re-rendered the Boltz-2 supplement with pdftotext -layout (poppler 26.08.0) and matched the text layer's recorded SHA-256. Re-read all 256 cells with a parser written for this review that does not import the extraction script, matching each result to its cell through its own source_locator, and separately read appendix tables 11, 12 and 14 from PNG renderings of PDF pages 29 and 30 at 160 dpi, and Ross Table 3 from the pinned XML markup. Checked printed value, numeric value, locator, metric concept, qualifier, direction, unit, uncertainty and the linked configuration, protocol and dataset, and that every N/A or '-' cell is recorded as missing with a reason.; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; reviewed at: 2026-10-22T13:40:00Z; artifact sha256: be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12262699/supplementaryFiles

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