Protocol

PLABench CASP16 L3000 affinity

Affinity prediction on CASP16 series L3000; structure-based models given the same AlphaFold3-predicted complex structures.

9 evaluations · 54 results

Overview

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9 recorded evaluations, 54 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 · 54 results. Different protocols are not a single leaderboard.

Protocol: PLABench CASP16 L3000 affinity · Dataset: CASP16 ligand affinity series L3000 (autotaxin)

Sorted by Concordance index (PLABench casp16-L3000) (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 casp16-L3000)	Modified squared correlation (PLABench casp16-L3000)	MSE (PLABench casp16-L3000)	Pearson (PLABench casp16-L3000)	RMSE (PLABench casp16-L3000)	Spearman (PLABench casp16-L3000)
Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.745 (best in column)	0.356	1.03	0.67 (best in column)	1.02	0.67 (best in column)
FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.744	0.432 (best in column)	0.73 (best in column)	0.661	0.854 (best in column)	0.669
LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.725	0.339	0.843	0.615	0.918	0.628
Graph_RG (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.723	0.312	1.07	0.576	1.04	0.632
MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.708	0.331	0.874	0.597	0.935	0.587
MFE (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.705	0.345	1.32	0.613	1.15	0.574
FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.674	0.178	1.32	0.462	1.15	0.49
DeepDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.668	0.2	1.58	0.485	1.26	0.475
LLF (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation	0.667	0.232	3.38	0.484	1.84	0.467

All 54 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: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.745 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 Boltz2 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 'Boltz2', series 'L3000', column 'CI' (text-layer line 832)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.03 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 Boltz2 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 'Boltz2', series 'L3000', column 'MSE' (text-layer line 832)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.67 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 Boltz2 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 'Boltz2', series 'L3000', column 'Pearson' (text-layer line 832)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.356 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 Boltz2 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 'Boltz2', series 'L3000', column 'rm2' (text-layer line 832)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.02 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 Boltz2 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 'Boltz2', series 'L3000', column 'RMSE' (text-layer line 832)
Configuration: Boltz2 (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.67 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 Boltz2 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 'Boltz2', series 'L3000', column 'Spearman' (text-layer line 832)
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: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.674 Concordance index (PLABench casp16-L3000) 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 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 'FlowDock', series 'L3000', column 'CI' (text-layer line 833)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.32 MSE (PLABench casp16-L3000) 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 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 'FlowDock', series 'L3000', column 'MSE' (text-layer line 833)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.462 Pearson (PLABench casp16-L3000) 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 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 'FlowDock', series 'L3000', column 'Pearson' (text-layer line 833)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.178 Modified squared correlation (PLABench casp16-L3000) 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 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 'FlowDock', series 'L3000', column 'rm2' (text-layer line 833)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	1.15 RMSE (PLABench casp16-L3000) 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 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 'FlowDock', series 'L3000', column 'RMSE' (text-layer line 833)
Configuration: FlowDock (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.49 Spearman (PLABench casp16-L3000) 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 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 'FlowDock', series 'L3000', column 'Spearman' (text-layer line 833)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.744 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 FLOWR.ROOT 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 'FLOWR.ROOT', series 'L3000', column 'CI' (text-layer line 834)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.73 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 FLOWR.ROOT 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 'FLOWR.ROOT', series 'L3000', column 'MSE' (text-layer line 834)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.661 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 FLOWR.ROOT 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 'FLOWR.ROOT', series 'L3000', column 'Pearson' (text-layer line 834)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.432 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 FLOWR.ROOT 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 'FLOWR.ROOT', series 'L3000', column 'rm2' (text-layer line 834)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.854 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 FLOWR.ROOT 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 'FLOWR.ROOT', series 'L3000', column 'RMSE' (text-layer line 834)
Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)	Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin)	0.669 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 FLOWR.ROOT 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 'FLOWR.ROOT', series 'L3000', column 'Spearman' (text-layer line 834)
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)

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

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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-casp16-l3000

areas: molecular-interactions
contexts: research
protocol: CASP16 L3000 series; MSE, RMSE, Pearson, Spearman, rm2 and CI as printed in Table 3
version: PLABench bioRxiv v1
limitations: Each series is a single target; Figure 2 states that each tau is computed over all ligands of a series, and Methods define the metrics over all test pairs.; Only one value per cell is printed; no uncertainty is reported in Tables 2-4.; Structure-based models received AlphaFold3-predicted structures, not crystal structures (Results).; Affinities in this series have a narrow high-affinity range, which the authors note makes RMSE and ranking metrics disagree.
source locator: Table 3, 'L3000' columns

Related records

part of: PLABench
uses data: CASP16 ligand affinity series L3000 (autotaxin)
assessment: Boltz2 on PLABench casp16-L3000
assessment: DeepDTA on PLABench casp16-L3000
assessment: FlowDock on PLABench casp16-L3000
assessment: FLOWR.ROOT on PLABench casp16-L3000
assessment: Graph_RG on PLABench casp16-L3000
assessment: LCDD-team on PLABench casp16-L3000
assessment: LLF on PLABench casp16-L3000
assessment: MFE on PLABench casp16-L3000
assessment: MixingDTA on PLABench casp16-L3000

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