Protein structures and congeneric ligand series with measured Kd, Ki or IC50 values converted to relative binding free energies in kcal/mol.
1 evaluation · 6 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: FEP+ with per-system manual protocol adjustment | Protocol: Public FEP benchmark, FEP+ accuracy against experiment Dataset: Curated public FEP benchmark compounds (Ross et al. 2023) | 0.91 [0.84, 0.98] MAE (edgewise mean unsigned error, weighted mean over FEP graphs, weight equal to edge count) kilocalorie-per-mole · lower Uncertainty: 95% CI 0.84 to 0.98. 95% confidence interval from bootstrap sampling over the pairs of experimental series or FEP+ graphs (Table 3 legend) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEP+ on the curated public FEP benchmark uc-leadopt-20261022-protocol-ross-fep-plus Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "Edgewise MUE (kcal mol−1)", column "FEP+ benchmark" |
| Configuration: FEP+ with per-system manual protocol adjustment | Protocol: Public FEP benchmark, FEP+ accuracy against experiment Dataset: Curated public FEP benchmark compounds (Ross et al. 2023) | 1.17 [1.08, 1.25] RMSE (edgewise, weighted mean over FEP graphs, weight equal to edge count) kilocalorie-per-mole · lower Uncertainty: 95% CI 1.08 to 1.25. 95% confidence interval from bootstrap sampling over the pairs of experimental series or FEP+ graphs (Table 3 legend) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEP+ on the curated public FEP benchmark uc-leadopt-20261022-protocol-ross-fep-plus Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "Edgewise RMSE (kcal mol−1)", column "FEP+ benchmark" |
| Configuration: FEP+ with per-system manual protocol adjustment | Protocol: Public FEP benchmark, FEP+ accuracy against experiment Dataset: Curated public FEP benchmark compounds (Ross et al. 2023) | 0.51 [0.48, 0.55] Kendall tau (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to compound count) unitless · higher Uncertainty: 95% CI 0.48 to 0.55. 95% confidence interval from bootstrap sampling over the pairs of experimental series or FEP+ graphs (Table 3 legend) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEP+ on the curated public FEP benchmark uc-leadopt-20261022-protocol-ross-fep-plus Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "Kendall τ", column "FEP+ benchmark" |
| Configuration: FEP+ with per-system manual protocol adjustment | Protocol: Public FEP benchmark, FEP+ accuracy against experiment Dataset: Curated public FEP benchmark compounds (Ross et al. 2023) | 0.98 [0.91, 1.05] MAE (pairwise mean unsigned error, weighted mean over series, weight equal to compound count) kilocalorie-per-mole · lower Uncertainty: 95% CI 0.91 to 1.05. 95% confidence interval from bootstrap sampling over the pairs of experimental series or FEP+ graphs (Table 3 legend) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEP+ on the curated public FEP benchmark uc-leadopt-20261022-protocol-ross-fep-plus Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "Pairwise MUE (kcal mol−1)", column "FEP+ benchmark" |
| Configuration: FEP+ with per-system manual protocol adjustment | Protocol: Public FEP benchmark, FEP+ accuracy against experiment Dataset: Curated public FEP benchmark compounds (Ross et al. 2023) | 1.25 [1.17, 1.33] RMSE (pairwise, weighted mean over series, weight equal to compound count) kilocalorie-per-mole · lower Uncertainty: 95% CI 1.17 to 1.33. 95% confidence interval from bootstrap sampling over the pairs of experimental series or FEP+ graphs (Table 3 legend) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEP+ on the curated public FEP benchmark uc-leadopt-20261022-protocol-ross-fep-plus Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "Pairwise RMSE (kcal mol−1)", column "FEP+ benchmark" |
| Configuration: FEP+ with per-system manual protocol adjustment | Protocol: Public FEP benchmark, FEP+ accuracy against experiment Dataset: Curated public FEP benchmark compounds (Ross et al. 2023) | 0.56 [0.51, 0.60] R² (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to compound count) unitless · higher Uncertainty: 95% CI 0.51 to 0.60. 95% confidence interval from bootstrap sampling over the pairs of experimental series or FEP+ graphs (Table 3 legend) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFEP+ on the curated public FEP benchmark uc-leadopt-20261022-protocol-ross-fep-plus Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "R2", column "FEP+ benchmark" |
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8 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Assay Mixed binding and functional assays reporting Kd, Ki or IC50 Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population 1,237 compounds over the 14 data sets listed in Table 2, spanning more than 50 proteins Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope note Measured affinities are converted to relative binding free energies under the paper's stated assumption that IC50, Ki and Kd ratios are interchangeable. Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location Table 2; Methods, 'Experimental data' Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split Whole collection; no training split because the evaluated method is not trained Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version As curated for Ross et al. 2023 after structural curation Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Protein structures and congeneric ligand series with measured Kd, Ki or IC50 values converted to relative binding free energies in kcal/mol. Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name Curated public FEP benchmark compounds (Ross et al. 2023) Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 2; Methods, 'Experimental data' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: uc-leadopt-20261022-data-fep-benchmark