Protocol

PLABench ChEMBL35 leakage-controlled affinity

Affinity prediction on the leakage-controlled ChEMBL35 set; no retraining.

Overview

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9 recorded evaluations, 63 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

9 evaluations · 63 results. Different protocols are not a single leaderboard.

Protocol: PLABench ChEMBL35 leakage-controlled affinity · Dataset: PLABench ChEMBL35 leakage-controlled test set

Sorted by Concordance index (PLABench chembl35) (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	Concordance index (PLABench chembl35)	Kendall tau (PLABench chembl35)	Modified squared correlation (PLABench chembl35)	MSE (PLABench chembl35)	Pearson (PLABench chembl35)	RMSE (PLABench chembl35)	Spearman (PLABench chembl35)
FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.632 (best in column)	0.264 (best in column)	0.168 (best in column)	0.931 (best in column)	0.392 (best in column)	0.928 (best in column)	0.374 (best in column)
Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.606	0.211	0.098	1.69	0.321	1.25	0.302
LLF (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.572	0.144	0.072	2.5	0.212	1.46	0.208
FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.56	0.12	0.051	2.22	0.188	1.37	0.173
MFE (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.556	0.111	0.048	1.63	0.177	1.21	0.162
MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.556	0.112	0.048	1.81	0.173	1.27	0.162
DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.551	0.103	0.045	2.17	0.153	1.39	0.151
LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.545	0.091	0.038	1.64	0.157	1.22	0.131
Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.544	0.089	0.035	1.97	0.146	1.34	0.128

All 63 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.606 Concordance index (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'CI' (text-layer line 1032)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.211 Kendall tau (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'Kendall' (text-layer line 1032)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	1.69 MSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'MSE' (text-layer line 1032)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.321 Pearson (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'Pearson' (text-layer line 1032)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.098 Modified squared correlation (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'rm2' (text-layer line 1032)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	1.25 RMSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'RMSE' (text-layer line 1032)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.302 Spearman (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Boltz2 on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'Boltz2', column 'Spearman' (text-layer line 1032)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.551 Concordance index (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'CI' (text-layer line 1038)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.103 Kendall tau (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'Kendall' (text-layer line 1038)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	2.17 MSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'MSE' (text-layer line 1038)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.153 Pearson (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'Pearson' (text-layer line 1038)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.045 Modified squared correlation (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'rm2' (text-layer line 1038)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	1.39 RMSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'RMSE' (text-layer line 1038)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.151 Spearman (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepDTA on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'DeepDTA', column 'Spearman' (text-layer line 1038)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.56 Concordance index (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'CI' (text-layer line 1033)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.12 Kendall tau (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'Kendall' (text-layer line 1033)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	2.22 MSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'MSE' (text-layer line 1033)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.188 Pearson (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'Pearson' (text-layer line 1033)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.051 Modified squared correlation (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'rm2' (text-layer line 1033)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	1.37 RMSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'RMSE' (text-layer line 1033)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.173 Spearman (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FlowDock on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FlowDock', column 'Spearman' (text-layer line 1033)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.632 Concordance index (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FLOWR.ROOT on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FLOWR.ROOT', column 'CI' (text-layer line 1034)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.264 Kendall tau (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FLOWR.ROOT on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FLOWR.ROOT', column 'Kendall' (text-layer line 1034)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.931 MSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FLOWR.ROOT on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FLOWR.ROOT', column 'MSE' (text-layer line 1034)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.392 Pearson (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FLOWR.ROOT on PLABench chembl35 lit-interactions-20261011-leakctl-protocol-chembl35 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 4, row 'FLOWR.ROOT', column 'Pearson' (text-layer line 1034)

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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Author-reported evaluations: 1
External evaluations: 8

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Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Original source · bioRxiv 10.64898/2026.09.17.752433v1 (posted 2026-09-23); 30-page PDF

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Technical metadata and extraction receipts

Stable ID: lit-interactions-20261011-leakctl-protocol-chembl35

areas: molecular-interactions
contexts: research
protocol: ChEMBL35 filtered test set; MSE, RMSE, Pearson, Spearman, Kendall, rm2 and CI as printed in Table 4
version: PLABench bioRxiv v1
limitations: Methods ('Evaluation metrics') define each metric over N target-ligand pairs, but the source does not state whether Table 4 pools all 4,862 pairs or averages per-target values.; Only one value per cell is printed; no uncertainty is reported in Tables 2-4.; The text describes this set as target-centric but does not state whether Table 4 pools all complexes or averages over targets.
source locator: Table 4

Related records

part of: PLABench
uses data: PLABench ChEMBL35 leakage-controlled test set
assessment: Boltz2 on PLABench chembl35
assessment: DeepDTA on PLABench chembl35
assessment: FlowDock on PLABench chembl35
assessment: FLOWR.ROOT on PLABench chembl35
assessment: Graph_RG on PLABench chembl35
assessment: LCDD-team on PLABench chembl35
assessment: LLF on PLABench chembl35
assessment: MFE on PLABench chembl35
assessment: MixingDTA on PLABench chembl35

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