Dataset

OpenFE subset of the public FEP benchmark

876 protein-ligand complexes drawn from hit-to-lead and lead optimisation campaigns with measured affinities.

Evaluation results

6 evaluations · 54 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.19 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 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 "BACPI", column "Kendall tau", sub-column "target avg." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.85 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 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 "BACPI", column "MAE", sub-column "cent." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	1.44 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 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 "BACPI", column "MAE", sub-column "non-cent." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.29 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 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 "BACPI", column "Pearson R", sub-column "target avg." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	1.21 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 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 "BACPI", column "PMAE", sub-column "target avg." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.67 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 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 "BACPI", column "Perc. within 1", sub-column "cent." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.4 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 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 "BACPI", column "Perc. within 1", sub-column "non-cent." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.94 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 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 "BACPI", column "Perc. within 2", sub-column "cent." (text-layer line 1693)
Configuration: BACPI as trained for the Boltz-2 affinity baselines	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.74 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 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 "BACPI", column "Perc. within 2", sub-column "non-cent." (text-layer line 1693)
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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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 checked Methods, coverage and source Boltz-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)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.46 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 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", column "Kendall tau", sub-column "target avg." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.64 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 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", column "MAE", sub-column "cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	1.22 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 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", column "MAE", sub-column "non-cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.62 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 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", column "Pearson R", sub-column "target avg." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.93 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 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", column "PMAE", sub-column "target avg." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.8 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 Boltz-2 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", column "Perc. within 1", sub-column "cent." (text-layer line 1690)
Configuration: Boltz-2 affinity prediction	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.49 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 Boltz-2 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", column "Perc. within 1", sub-column "non-cent." (text-layer line 1690)

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Inspect claims, sources and review details

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6 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 876 protein-ligand complexes Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'We evaluate model performance on the following held-out affinity test sets' 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
Source location Appendix D.2.1, 'We evaluate model performance on the following held-out affinity test sets' Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'We evaluate model performance on the following held-out affinity test sets' 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, 'We evaluate model performance on the following held-out affinity test sets' 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 Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'We evaluate model performance on the following held-out affinity test sets' 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 876 protein-ligand complexes drawn from hit-to-lead and lead optimisation campaigns with measured affinities. Context-only references	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Original source ↗ Appendix D.2.1, 'We evaluate model performance on the following held-out affinity test sets' 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 OpenFE 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, 'We evaluate model performance on the following held-out affinity test sets' 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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Sources and history

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

1 source record and release history

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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Technical metadata and extraction receipts

Stable ID: uc-leadopt-20261022-data-fep-openfe-subset

areas: molecular-interactions
contexts: research
version: Subset of the FEP+ benchmark as used in the Boltz-2 supplement
split: Held-out affinity test set
population: 876 protein-ligand complexes
source locator: Appendix D.2.1, 'We evaluate model performance on the following held-out affinity test sets'
missing metadata: total targets: reason: unreported; note: The supplement states the complex count but not how many targets or assays the subset covers
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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data: GAT on the FEP+ benchmark OpenFE subset
data: OpenFE on the FEP+ benchmark OpenFE subset
uses data: FEP+ benchmark OpenFE subset, affinity ranking

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