LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench)
Configuration of LCDD-team: Published checkpoint applied without retraining; given AlphaFold3-predicted complex structures.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench CASP16 L1000 affinity, CASP16 ligand affinity series L1000 (chymase) | 0.5 | Not reported | Not reported | Not reported | 0 | Not reported | Not reported | 1.14 | Not reported | Not reported | 0.054 | Not reported | Not reported | 1.07 | Not reported | Not reported | 0.022 | Not reported | Not reported |
| LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench CASP16 L3000 affinity, CASP16 ligand affinity series L3000 (autotaxin) | Not reported | 0.725 | Not reported | Not reported | Not reported | 0.339 | Not reported | Not reported | 0.843 | Not reported | Not reported | 0.615 | Not reported | Not reported | 0.918 | Not reported | Not reported | 0.628 | Not reported |
| LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench ChEMBL35 leakage-controlled affinity, PLABench ChEMBL35 leakage-controlled test set | Not reported | Not reported | 0.545 | 0.091 | Not reported | Not reported | 0.038 | Not reported | Not reported | 1.64 | Not reported | Not reported | 0.157 | Not reported | Not reported | 1.22 | Not reported | Not reported | 0.131 |
All 19 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.5 Concordance index (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L1000', column 'CI' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 1.14 MSE (PLABench casp16-L1000) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L1000', column 'MSE' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.054 Pearson (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L1000', column 'Pearson' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0 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 checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L1000', column 'rm2' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 1.07 RMSE (PLABench casp16-L1000) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L1000', column 'RMSE' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.022 Spearman (PLABench casp16-L1000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L1000', column 'Spearman' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.725 Concordance index (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L3000', column 'CI' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.843 MSE (PLABench casp16-L3000) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L3000', column 'MSE' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.615 Pearson (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L3000', column 'Pearson' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.339 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 checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L3000', column 'rm2' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.918 RMSE (PLABench casp16-L3000) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L3000', column 'RMSE' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.628 Spearman (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', series 'L3000', column 'Spearman' (text-layer line 836) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.545 Concordance index (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'CI' (text-layer line 1036) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.091 Kendall tau (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'Kendall' (text-layer line 1036) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 1.64 MSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'MSE' (text-layer line 1036) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.157 Pearson (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'Pearson' (text-layer line 1036) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.038 Modified squared correlation (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'rm2' (text-layer line 1036) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 1.22 RMSE (PLABench chembl35) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'RMSE' (text-layer line 1036) |
| Configuration: LCDD-team (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.131 Spearman (PLABench chembl35) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLCDD-team 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 'LCDD-team', column 'Spearman' (text-layer line 1036) |
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- 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
Technical metadata and extraction receipts
Stable ID: lit-interactions-20261011-leakctl-config-lcdd-team-casp16-chembl35
- areas
- molecular-interactions
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- LCDD-team
- 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
- LCDD-team as evaluated in PLABench (structure-based).
Related records
- configuration of: LCDD-team
- system: LCDD-team on PLABench casp16-L1000
- system: LCDD-team on PLABench casp16-L3000
- system: LCDD-team on PLABench chembl35