Configuration

DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)

Configuration of DeepDTA: Retrained by the benchmark authors on the PDBbind v2020 refined set (CASF and CSAR overlaps and censored entries removed; 4,465 training and 497 validation complexes; random 90/10 split with early stopping; longest single chain); applied to CASP16 and ChEMBL35 without further training.

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)
DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	PLABench CASP16 L1000 affinity, CASP16 ligand affinity series L1000 (chymase)	0.566	Not reported	Not reported	Not reported	-0.008	Not reported	Not reported	1.02	Not reported	Not reported	-0.195	Not reported	Not reported	1.01	Not reported	Not reported	0.201	Not reported	Not reported
DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	PLABench CASP16 L3000 affinity, CASP16 ligand affinity series L3000 (autotaxin)	Not reported	0.668	Not reported	Not reported	Not reported	0.2	Not reported	Not reported	1.58	Not reported	Not reported	0.485	Not reported	Not reported	1.26	Not reported	Not reported	0.475	Not reported
DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	PLABench ChEMBL35 leakage-controlled affinity, PLABench ChEMBL35 leakage-controlled test set	Not reported	Not reported	0.551	0.103	Not reported	Not reported	0.045	Not reported	Not reported	2.17	Not reported	Not reported	0.153	Not reported	Not reported	1.39	Not reported	Not reported	0.151

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: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	0.566 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 DeepDTA 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 'DeepDTA', series 'L1000', column 'CI' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	1.02 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 DeepDTA 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 'DeepDTA', series 'L1000', column 'MSE' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	-0.195 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 DeepDTA 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 'DeepDTA', series 'L1000', column 'Pearson' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	-0.008 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 DeepDTA 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 'DeepDTA', series 'L1000', column 'rm2' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	1.01 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 DeepDTA 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 'DeepDTA', series 'L1000', column 'RMSE' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase)	0.201 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 DeepDTA 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 'DeepDTA', series 'L1000', column 'Spearman' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.668 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 DeepDTA 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 'DeepDTA', series 'L3000', column 'CI' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.58 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 DeepDTA 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 'DeepDTA', series 'L3000', column 'MSE' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.485 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 DeepDTA 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 'DeepDTA', series 'L3000', column 'Pearson' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.2 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 DeepDTA 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 'DeepDTA', series 'L3000', column 'rm2' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.26 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 DeepDTA 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 'DeepDTA', series 'L3000', column 'RMSE' (text-layer line 838)
Configuration: DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.475 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 DeepDTA 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 'DeepDTA', series 'L3000', column 'Spearman' (text-layer line 838)
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)

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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-deepdta-casp16-chembl35

areas: molecular-interactions
contexts: research
method types: supervised_machine_learning
reported name: DeepDTA
foundation model eligible: false
parameters: Retrained by the benchmark authors on the PDBbind v2020 refined set (CASF and CSAR overlaps and censored entries removed; 4,465 training and 497 validation complexes; random 90/10 split with early stopping; longest single chain); applied to CASP16 and ChEMBL35 without further training (Methods, 'PDBbind v2020 dataset')
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: DeepDTA as evaluated in PLABench (sequence-based).

Related records

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

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