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1 evaluation · 6 results. Different protocols are not a single leaderboard.
Protocol: Repeat-assay reproducibility of relative binding free energies · Dataset: Repeat-assay affinity survey (Ross et al. 2023)
Sorted by Kendall tau (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to 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 | Kendall tau (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to compound count) | MAE (edgewise mean unsigned error, weighted mean over FEP graphs, weight equal to edge count) | MAE (pairwise mean unsigned error, weighted mean over series, weight equal to compound count) | R² (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to compound count) | RMSE (edgewise, weighted mean over FEP graphs, weight equal to edge count) | RMSE (pairwise, weighted mean over series, weight equal to compound count) |
|---|---|---|---|---|---|---|
| Second independent assay as the predictorEvaluation | 0.71 [0.65, 0.74] | N/A | 0.67 [0.61, 0.83] | 0.79 [0.75, 0.82] | N/A | 0.91 [0.83, 1.11] |
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Second independent assay as the predictor | Protocol: Repeat-assay reproducibility of relative binding free energies Dataset: Repeat-assay affinity survey (Ross et al. 2023) | N/A MAE (edgewise mean unsigned error, weighted mean over FEP graphs, weight equal to edge count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceIndependent repeat affinity assay on the repeat-assay survey uc-leadopt-20261022-protocol-ross-experimental-survey 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 "Experimental survey" |
| Configuration: Second independent assay as the predictor | Protocol: Repeat-assay reproducibility of relative binding free energies Dataset: Repeat-assay affinity survey (Ross et al. 2023) | N/A RMSE (edgewise, weighted mean over FEP graphs, weight equal to edge count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceIndependent repeat affinity assay on the repeat-assay survey uc-leadopt-20261022-protocol-ross-experimental-survey 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 "Experimental survey" |
| Configuration: Second independent assay as the predictor | Protocol: Repeat-assay reproducibility of relative binding free energies Dataset: Repeat-assay affinity survey (Ross et al. 2023) | 0.71 [0.65, 0.74] Kendall tau (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to compound count) unitless · higher Uncertainty: 95% CI 0.65 to 0.74. 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 sourceIndependent repeat affinity assay on the repeat-assay survey uc-leadopt-20261022-protocol-ross-experimental-survey Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "Kendall τ", column "Experimental survey" |
| Configuration: Second independent assay as the predictor | Protocol: Repeat-assay reproducibility of relative binding free energies Dataset: Repeat-assay affinity survey (Ross et al. 2023) | 0.67 [0.61, 0.83] MAE (pairwise mean unsigned error, weighted mean over series, weight equal to compound count) kilocalorie-per-mole · lower Uncertainty: 95% CI 0.61 to 0.83. 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 sourceIndependent repeat affinity assay on the repeat-assay survey uc-leadopt-20261022-protocol-ross-experimental-survey 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 "Experimental survey" |
| Configuration: Second independent assay as the predictor | Protocol: Repeat-assay reproducibility of relative binding free energies Dataset: Repeat-assay affinity survey (Ross et al. 2023) | 0.91 [0.83, 1.11] RMSE (pairwise, weighted mean over series, weight equal to compound count) kilocalorie-per-mole · lower Uncertainty: 95% CI 0.83 to 1.11. 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 sourceIndependent repeat affinity assay on the repeat-assay survey uc-leadopt-20261022-protocol-ross-experimental-survey 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 "Experimental survey" |
| Configuration: Second independent assay as the predictor | Protocol: Repeat-assay reproducibility of relative binding free energies Dataset: Repeat-assay affinity survey (Ross et al. 2023) | 0.79 [0.75, 0.82] R² (of the cycle-closure-corrected absolute free energies, weighted mean over series, weight equal to compound count) unitless · higher Uncertainty: 95% CI 0.75 to 0.82. 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 sourceIndependent repeat affinity assay on the repeat-assay survey uc-leadopt-20261022-protocol-ross-experimental-survey Aggregation: Not reported The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Table 3, row "R2", column "Experimental survey" |
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Repeat-assay reproducibility of relative binding free energies
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Not applicable: a second independent assay is used as the estimate Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Weighted by the number of compounds in each assay comparison; confidence intervals by bootstrap sampling over each assay comparison Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version As curated for Ross et al. 2023 Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Curated protein structures and congeneric ligand series with measured affinities Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: metric implementation Pairwise errors over every ligand pair in a graph; edgewise errors over the graph's edges; R2 and Kendall tau of the cycle-closure-corrected absolute free energies (Methods, 'Accuracy metrics') Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: population 1,867 compounds across 62 assay comparisons (26 binding vs binding, 30 binding vs functional, 6 functional vs functional) Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: protocol id uc-leadopt-20261022-protocol-ross-experimental-survey Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: split Whole collection; the assessed workflow is not trained Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Origin author_reported Context-only references | The maximal and current accuracy of rigorous protein-ligand binding free energy calculations Table 3, column 'Experimental survey' Version: Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784 | not individually reviewed No individual claim review recorded author reported 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-eval-ross-t3-experimental-survey