Repeat-assay reproducibility of relative binding free energies
Compares relative binding free energies for the same compounds measured in two independent affinity assays, reporting compound-weighted averages with bootstrap confidence intervals.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
1 recorded evaluation, 6 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
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] |
All 6 result rows with coverage, uncertainty and sources
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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" |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
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Recorded evaluations
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Baseline coverage
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- Author-reported evaluations
- 1
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- The maximal and current accuracy of rigorous protein-ligand binding free energy calculations · Original source · Communications Chemistry 6:222 (2023); Europe PMC full-text XML snapshot PMC10576784
Technical metadata and extraction receipts
Stable ID: uc-leadopt-20261022-protocol-ross-experimental-survey
- areas
- molecular-interactions
- contexts
- research
- protocol
- Pairwise RMSE and MUE in kcal/mol, coefficient of determination and Kendall tau between two independent assays of the same compounds, weighted by the number of compounds in each assay comparison
- version
- Ross et al. 2023 Table 3, 'Experimental survey' column
- aggregation
- Weighted by the number of compounds in each assay comparison; confidence intervals by bootstrap sampling over each assay comparison (Results, 'Comparing the accuracy of FEP+ with experimental reproducibility')
- metric definition
- The same pairwise metric definitions as the FEP+ column, so that the two columns are comparable; the paper states 'The pairwise errors and correlation metrics of the experimental survey and FEP+ benchmark are directly comparable'
- uncertainty reporting
- definition: 95% confidence intervals from bootstrap sampling over the pairs of experimental series (Table 3 legend)
- heldout test
- Not applicable: no method is being scored
- source locator
- Table 3, column 'Experimental survey'
- limitations
- This protocol measures assay reproducibility, not a prediction method. It bounds the accuracy any method could reach on this kind of data; it does not rank analogues.; Edgewise errors have no equivalent here, because they depend on the topology of an FEP perturbation graph; Table 3 prints N/A for both.; The survey pools publicly reported assays with Schrodinger internal project data; the weighted experimental values carry wider bootstrap intervals than the FEP+ values.; Only 6 functional-vs-functional assay comparisons contribute, which the paper says makes that category's weighted means less meaningful.
- 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: f371d2e373306588d11b695b8de21b253a90293d6a15884f635bcf927bdebb1d; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10576784/fullTextXML