Configuration

Second independent assay as the predictor

Treats one assay's measured affinities as the prediction of another assay's measured affinities for the same compounds, which gives the reproducibility ceiling for the same metrics.

1 evaluation · 6 results

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Evaluations and results

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 checked Methods, coverage and source Independent 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 checked Methods, coverage and source Independent 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 checked Methods, coverage and source Independent 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 checked Methods, coverage and source Independent 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 checked Methods, coverage and source Independent 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 checked Methods, coverage and source Independent 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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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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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

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Technical metadata and extraction receipts

Stable ID: uc-leadopt-20261022-config-experimental-reassay

areas: molecular-interactions
contexts: research
configuration type: reported_configuration
reported name: Experimental survey
version: As surveyed for Ross et al. 2023
access reuse: Publicly reported assays plus Schrodinger internal project data; the internal data is not public.
source locator: Table 3, column 'Experimental survey'
limitations: This is an experimental reference, not a predictive method. Its values bound what any method could achieve on this kind of data.
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

Related records

configuration of: Independent repeat affinity assay
system: Independent repeat affinity assay on the repeat-assay survey

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