Configuration

OpenFE under a fixed automated protocol

OpenFE run with its default settings and no per-system adjustment, which the comparison treats as the automated open-source free energy arm.

2 evaluations · 19 results

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Evaluations and results

2 evaluations · 19 results. Different protocols are not a single leaderboard.

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	Protocol and dataset	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)	Accelerator time (per-method cost as printed beside the accuracy columns)
OpenFE under a fixed automated protocolEvaluation	FEP+ benchmark four-target subset, affinity ranking and cost, Four-target subset of the public FEP benchmark	0.51 (best in column)	0.75 (best in column)	N/A	1.09 (best in column)	0.66 (best in column)	0.7 (best in column)	N/A	0.98 (best in column)	N/A	6-12 GPU hours
OpenFE under a fixed automated protocolEvaluation	FEP+ benchmark OpenFE subset, affinity ranking, OpenFE subset of the public FEP benchmark	0.47	0.94	N/A	1.37	0.63	0.65	N/A	0.91	N/A	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.47 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 OpenFE 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 "OpenFE", column "Kendall tau", sub-column "target avg." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.94 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 OpenFE 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 "OpenFE", column "MAE", sub-column "cent." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	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	Evaluation origin not reported · Source checked Methods, coverage and source OpenFE 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 "OpenFE", column "MAE", sub-column "non-cent." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.63 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 OpenFE 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 "OpenFE", column "Pearson R", sub-column "target avg." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	1.37 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 OpenFE 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 "OpenFE", column "PMAE", sub-column "target avg." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.65 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 OpenFE 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 "OpenFE", column "Perc. within 1", sub-column "cent." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	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	Evaluation origin not reported · Source checked Methods, coverage and source OpenFE 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 "OpenFE", column "Perc. within 1", sub-column "non-cent." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark OpenFE subset, affinity ranking Dataset: OpenFE subset of the public FEP benchmark	0.91 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 OpenFE 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 "OpenFE", column "Perc. within 2", sub-column "cent." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	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	Evaluation origin not reported · Source checked Methods, coverage and source OpenFE 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 "OpenFE", column "Perc. within 2", sub-column "non-cent." (text-layer line 1694)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.51 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 OpenFE 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 "OpenFE", column "Kendall tau", sub-column "target avg." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.75 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 OpenFE 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 "OpenFE", column "MAE", sub-column "cent." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	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	Evaluation origin not reported · Source checked Methods, coverage and source OpenFE 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 "OpenFE", column "MAE", sub-column "non-cent." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.66 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 OpenFE 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 "OpenFE", column "Pearson R", sub-column "target avg." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	1.09 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 OpenFE 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 "OpenFE", column "PMAE", sub-column "target avg." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	6-12 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 OpenFE 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 "OpenFE", column "time" (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark	0.7 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 OpenFE 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 "OpenFE", column "Perc. within 1", sub-column "cent." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target 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	Evaluation origin not reported · Source checked Methods, coverage and source OpenFE 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 "OpenFE", column "Perc. within 1", sub-column "non-cent." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	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 OpenFE 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 "OpenFE", column "Perc. within 2", sub-column "cent." (text-layer line 1710)
Configuration: OpenFE under a fixed automated protocol	Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target 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	Evaluation origin not reported · Source checked Methods, coverage and source OpenFE 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 "OpenFE", column "Perc. within 2", sub-column "non-cent." (text-layer line 1710)

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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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Technical metadata and extraction receipts

Stable ID: uc-leadopt-20261022-config-openfe

areas: molecular-interactions
contexts: research
method types: conventional_pipeline
configuration type: reported_configuration
reported name: OpenFE
version: Not printed; the supplement cites Gowers et al. 2023 for the method and Horton 2025 for the results
access reuse: Open source.
source locator: Tables 11 and 12, row 'OpenFE'; appendix D.2.2
limitations: The cited source for these results is a blog post, which is not a primary source under this repository's rules and was not retrieved. The peer-reviewed OpenFE assessment (doi 10.1021/acs.jcim.6c00089) is behind an ACS paywall and was not retrieved.
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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