Configuration

Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)

Configuration of Graph_RG: Published checkpoint applied without retraining; given AlphaFold3-predicted complex structures.

3 evaluations · 19 results

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Evaluations and results

3 evaluations · 19 results. Different protocols are not a single leaderboard.

Sorted by Concordance index (PLABench casp16-L1000) (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	Protocol and dataset	Concordance index (PLABench casp16-L1000)	Concordance index (PLABench casp16-L3000)	Concordance index (PLABench chembl35)	Kendall tau (PLABench chembl35)	Modified squared correlation (PLABench casp16-L1000)	Modified squared correlation (PLABench casp16-L3000)	Modified squared correlation (PLABench chembl35)	MSE (PLABench casp16-L1000)	MSE (PLABench casp16-L3000)	MSE (PLABench chembl35)	Pearson (PLABench casp16-L1000)	Pearson (PLABench casp16-L3000)	Pearson (PLABench chembl35)	RMSE (PLABench casp16-L1000)	RMSE (PLABench casp16-L3000)	RMSE (PLABench chembl35)	Spearman (PLABench casp16-L1000)	Spearman (PLABench casp16-L3000)	Spearman (PLABench chembl35)
Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	PLABench CASP16 L1000 affinity, CASP16 ligand affinity series L1000 (chymase)	0.625	Not reported	Not reported	Not reported	-0.02	Not reported	Not reported	1.31	Not reported	Not reported	0.406	Not reported	Not reported	1.14	Not reported	Not reported	0.404	Not reported	Not reported
Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	PLABench CASP16 L3000 affinity, CASP16 ligand affinity series L3000 (autotaxin)	Not reported	0.723	Not reported	Not reported	Not reported	0.312	Not reported	Not reported	1.07	Not reported	Not reported	0.576	Not reported	Not reported	1.04	Not reported	Not reported	0.632	Not reported
Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	PLABench ChEMBL35 leakage-controlled affinity, PLABench ChEMBL35 leakage-controlled test set	Not reported	Not reported	0.544	0.089	Not reported	Not reported	0.035	Not reported	Not reported	1.97	Not reported	Not reported	0.146	Not reported	Not reported	1.34	Not reported	Not reported	0.128

All 19 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	0.625 Concordance index (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L1000 lit-interactions-20261011-leakctl-protocol-casp16-l1000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L1000', column 'CI' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	1.31 MSE (PLABench casp16-L1000) 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 Graph_RG on PLABench casp16-L1000 lit-interactions-20261011-leakctl-protocol-casp16-l1000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L1000', column 'MSE' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	0.406 Pearson (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L1000 lit-interactions-20261011-leakctl-protocol-casp16-l1000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L1000', column 'Pearson' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	-0.02 Modified squared correlation (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L1000 lit-interactions-20261011-leakctl-protocol-casp16-l1000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L1000', column 'rm2' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	1.14 RMSE (PLABench casp16-L1000) 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 Graph_RG on PLABench casp16-L1000 lit-interactions-20261011-leakctl-protocol-casp16-l1000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L1000', column 'RMSE' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	0.404 Spearman (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L1000 lit-interactions-20261011-leakctl-protocol-casp16-l1000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L1000', column 'Spearman' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.723 Concordance index (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L3000 lit-interactions-20261011-leakctl-protocol-casp16-l3000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L3000', column 'CI' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.07 MSE (PLABench casp16-L3000) 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 Graph_RG on PLABench casp16-L3000 lit-interactions-20261011-leakctl-protocol-casp16-l3000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L3000', column 'MSE' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.576 Pearson (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L3000 lit-interactions-20261011-leakctl-protocol-casp16-l3000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L3000', column 'Pearson' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.312 Modified squared correlation (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L3000 lit-interactions-20261011-leakctl-protocol-casp16-l3000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L3000', column 'rm2' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.04 RMSE (PLABench casp16-L3000) 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 Graph_RG on PLABench casp16-L3000 lit-interactions-20261011-leakctl-protocol-casp16-l3000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L3000', column 'RMSE' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.632 Spearman (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Graph_RG on PLABench casp16-L3000 lit-interactions-20261011-leakctl-protocol-casp16-l3000 Aggregation: Not reported Leakage-controlled benchmarking reveals generalization limits of deep learning for protein-ligand binding affinity prediction · Table 3, row 'Graph_RG', series 'L3000', column 'Spearman' (text-layer line 835)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.544 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 Graph_RG 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 'Graph_RG', column 'CI' (text-layer line 1035)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.089 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 Graph_RG 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 'Graph_RG', column 'Kendall' (text-layer line 1035)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	1.97 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 Graph_RG 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 'Graph_RG', column 'MSE' (text-layer line 1035)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.146 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 Graph_RG 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 'Graph_RG', column 'Pearson' (text-layer line 1035)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.035 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 Graph_RG 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 'Graph_RG', column 'rm2' (text-layer line 1035)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	1.34 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 Graph_RG 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 'Graph_RG', column 'RMSE' (text-layer line 1035)
Configuration: Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set	0.128 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 Graph_RG 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 'Graph_RG', column 'Spearman' (text-layer line 1035)

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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-config-graph-rg-casp16-chembl35

areas: molecular-interactions
contexts: research
method types: supervised_machine_learning
reported name: Graph_RG
foundation model eligible: false
parameters: Published checkpoint applied without retraining; given AlphaFold3-predicted complex structures
source locator: Table 1; Methods; Tables 3 and 4
access reuse: Not stated per model in the source; see each model's release
missing metadata: version: reason: unreported; note: No checkpoint version printed
provenance note: Graph_RG as evaluated in PLABench (structure-based).

Related records

configuration of: Graph_RG
system: Graph_RG on PLABench casp16-L1000
system: Graph_RG on PLABench casp16-L3000
system: Graph_RG on PLABench chembl35

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