MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench)
Configuration of MixingDTA: 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.
Overview
An explanatory profile has not yet been reviewed for this record.
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) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench CASP16 L1000 affinity, CASP16 ligand affinity series L1000 (chymase) | 0.537 | Not reported | Not reported | Not reported | -0.004 | Not reported | Not reported | 2.88 | Not reported | Not reported | -0.085 | Not reported | Not reported | 1.7 | Not reported | Not reported | 0.113 | Not reported | Not reported |
| MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench CASP16 L3000 affinity, CASP16 ligand affinity series L3000 (autotaxin) | Not reported | 0.708 | Not reported | Not reported | Not reported | 0.331 | Not reported | Not reported | 0.874 | Not reported | Not reported | 0.597 | Not reported | Not reported | 0.935 | Not reported | Not reported | 0.587 | Not reported |
| MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench)Evaluation | PLABench ChEMBL35 leakage-controlled affinity, PLABench ChEMBL35 leakage-controlled test set | Not reported | Not reported | 0.556 | 0.112 | Not reported | Not reported | 0.048 | Not reported | Not reported | 1.81 | Not reported | Not reported | 0.173 | Not reported | Not reported | 1.27 | Not reported | Not reported | 0.162 |
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: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.537 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 sourceMixingDTA 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 'MixingDTA', series 'L1000', column 'CI' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 2.88 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 sourceMixingDTA 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 'MixingDTA', series 'L1000', column 'MSE' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | -0.085 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 sourceMixingDTA 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 'MixingDTA', series 'L1000', column 'Pearson' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | -0.004 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 sourceMixingDTA 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 'MixingDTA', series 'L1000', column 'rm2' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 1.7 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 sourceMixingDTA 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 'MixingDTA', series 'L1000', column 'RMSE' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L1000 affinity Dataset: CASP16 ligand affinity series L1000 (chymase) | 0.113 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 sourceMixingDTA 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 'MixingDTA', series 'L1000', column 'Spearman' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.708 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 sourceMixingDTA 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 'MixingDTA', series 'L3000', column 'CI' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.874 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 sourceMixingDTA 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 'MixingDTA', series 'L3000', column 'MSE' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.597 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 sourceMixingDTA 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 'MixingDTA', series 'L3000', column 'Pearson' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.331 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 sourceMixingDTA 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 'MixingDTA', series 'L3000', column 'rm2' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.935 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 sourceMixingDTA 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 'MixingDTA', series 'L3000', column 'RMSE' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench CASP16 L3000 affinity Dataset: CASP16 ligand affinity series L3000 (autotaxin) | 0.587 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 sourceMixingDTA 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 'MixingDTA', series 'L3000', column 'Spearman' (text-layer line 840) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.556 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 sourceMixingDTA 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 'MixingDTA', column 'CI' (text-layer line 1040) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.112 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 sourceMixingDTA 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 'MixingDTA', column 'Kendall' (text-layer line 1040) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 1.81 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 sourceMixingDTA 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 'MixingDTA', column 'MSE' (text-layer line 1040) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.173 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 sourceMixingDTA 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 'MixingDTA', column 'Pearson' (text-layer line 1040) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.048 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 sourceMixingDTA 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 'MixingDTA', column 'rm2' (text-layer line 1040) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 1.27 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 sourceMixingDTA 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 'MixingDTA', column 'RMSE' (text-layer line 1040) |
| Configuration: MixingDTA (CASP16 and ChEMBL35 evaluation, PLABench) | Protocol: PLABench ChEMBL35 leakage-controlled affinity Dataset: PLABench ChEMBL35 leakage-controlled test set | 0.162 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 sourceMixingDTA 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 'MixingDTA', column 'Spearman' (text-layer line 1040) |
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
Use this configuration
How it works, versions and access
Additional methodological details, versions and access terms have not yet been extracted into a structured profile for this configuration. Consult the linked sources and evaluation records below.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
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-mixingdta-casp16-chembl35
- areas
- molecular-interactions
- contexts
- research
- method types
- foundation_model
- reported name
- MixingDTA
- foundation model eligible
- true
- 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
- MixingDTA as evaluated in PLABench (sequence-based).
Related records
- configuration of: MixingDTA
- system: MixingDTA on PLABench casp16-L1000
- system: MixingDTA on PLABench casp16-L3000
- system: MixingDTA on PLABench chembl35