FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)
Configuration of FLOWR.ROOT: 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) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench CASP16 L1000 affinity, CASP16 ligand affinity series L1000 (chymase) | 0.544 | Not reported | Not reported | Not reported | 0.03 | Not reported | Not reported | 1.38 | Not reported | Not reported | 0.222 | Not reported | Not reported | 1.18 | Not reported | Not reported | 0.162 | Not reported | Not reported |
| FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench CASP16 L3000 affinity, CASP16 ligand affinity series L3000 (autotaxin) | Not reported | 0.744 | Not reported | Not reported | Not reported | 0.432 | Not reported | Not reported | 0.73 | Not reported | Not reported | 0.661 | Not reported | Not reported | 0.854 | Not reported | Not reported | 0.669 | Not reported |
| FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench ChEMBL35 leakage-controlled affinity, PLABench ChEMBL35 leakage-controlled test set | Not reported | Not reported | 0.632 | 0.264 | Not reported | Not reported | 0.168 | Not reported | Not reported | 0.931 | Not reported | Not reported | 0.392 | Not reported | Not reported | 0.928 | Not reported | Not reported | 0.374 |
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: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.544 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 sourceFLOWR.ROOT 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 'FLOWR.ROOT', series 'L1000', column 'CI' (text-layer line 834) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 1.38 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 sourceFLOWR.ROOT 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 'FLOWR.ROOT', series 'L1000', column 'MSE' (text-layer line 834) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.222 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 sourceFLOWR.ROOT 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 'FLOWR.ROOT', series 'L1000', column 'Pearson' (text-layer line 834) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.03 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 sourceFLOWR.ROOT 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 'FLOWR.ROOT', series 'L1000', column 'rm2' (text-layer line 834) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 1.18 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 sourceFLOWR.ROOT 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 'FLOWR.ROOT', series 'L1000', column 'RMSE' (text-layer line 834) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.162 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 sourceFLOWR.ROOT 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 'FLOWR.ROOT', series 'L1000', column 'Spearman' (text-layer line 834) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.744 Concordance index (PLABench casp16-L3000) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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: 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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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 checkedMethods, coverage and sourceFLOWR.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) |
| Configuration: FLOWR.ROOT (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.168 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 sourceFLOWR.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 'rm2' (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 | 0.928 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 sourceFLOWR.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 'RMSE' (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 | 0.374 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 sourceFLOWR.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 'Spearman' (text-layer line 1034) |
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
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Evidence
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Evidence table
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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-flowr-root-casp16-chembl35
- areas
- molecular-interactions
- contexts
- research
- method types
- foundation_model
- reported name
- FLOWR.ROOT
- foundation model eligible
- true
- 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
- FLOWR.ROOT as evaluated in PLABench (structure-based).
Related records
- configuration of: FLOWR.ROOT
- system: FLOWR.ROOT on PLABench casp16-L1000
- system: FLOWR.ROOT on PLABench casp16-L3000
- system: FLOWR.ROOT on PLABench chembl35