ABFE protocol optimised on the four-target subset
The absolute binding free energy protocol run on the four-target subset with settings that were optimised on that same data.
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Evaluations and results
1 evaluation · 10 results. Different protocols are not a single leaderboard.
Protocol: FEP+ benchmark four-target subset, affinity ranking and cost · Dataset: Four-target subset of the public FEP benchmark
Sorted by Accelerator time (per-method cost as printed beside the accuracy columns) (lower 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 | Accelerator time (per-method cost as printed beside the accuracy columns) | 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) |
|---|---|---|---|---|---|---|---|---|---|---|
| ABFE protocol optimised on the four-target subsetEvaluation | >20 GPU hours | 0.54 | 0.65 | 2.47 | 0.95 | 0.75 | 0.79 | 0.11 | 0.98 | 0.4 |
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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)
Technical metadata and extraction receipts
Stable ID: uc-leadopt-20261022-config-abfe
- areas
- molecular-interactions
- contexts
- research
- method types
- conventional_pipeline
- configuration type
- reported_configuration
- reported name
- ABFE
- version
- Not printed; the supplement cites Wu et al. 2025
- source locator
- Table 12, row 'ABFE'; appendix D.2.2
- limitations
- The supplement states the ABFE results 'may also represent an optimistic estimate of its prospective performance given that the protocol was optimized based this dataset'.
- 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
Related records
- configuration of: ABFE protocol (Wu et al. 2025)
- subject: ABFE protocol optimised on the data it is scored on
- system: ABFE on the FEP+ benchmark four-target subset