Strengths and considerations
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Configuration
K DEEP · 0.0001
K DEEP as evaluated in the cited study. K_DEEP reimplemented by AK-score authors in Keras 2.2.4 / TensorFlow 1.13.1; Table-specific network configuration; learning rate 0.0001
Sources
AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAEOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Evaluations and results
4 evaluations · 9 results. Different protocols are not a single leaderboard.
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: K DEEP · 0.0001 | Protocol: PDBbind-2016 core set (Protein–ligand binding affinity scoring) Dataset: PDBbind-2016 core set | 1.13 MAE kcal/mol · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: PDBbind-2016 core set Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAE |
| Configuration: K DEEP · 0.0001 | Protocol: PDBbind-2016 core set (Protein–ligand binding affinity scoring) Dataset: PDBbind-2016 core set | 1.46 RMSE kcal/mol · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: PDBbind-2016 core set Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 4: PDBbind-2016 core set RMSE |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 docking (Protein–ligand binding affinity scoring) Dataset: CASF-2016 docking | 24.8% Top 1 success percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 docking Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 ranking (Protein–ligand binding affinity scoring) Dataset: CASF-2016 ranking | 0.559 Predictive Index unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 ranking Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 6: CASF-2016 ranking Predictive Index |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 docking (Protein–ligand binding affinity scoring) Dataset: CASF-2016 docking | 38.5% Top 2 success percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 docking Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 8: CASF-2016 docking Top 2 success |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 ranking (Protein–ligand binding affinity scoring) Dataset: CASF-2016 ranking | 0.435 Kendall tau unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 ranking Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 5: CASF-2016 ranking Kendall tau |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 scoring (Protein–ligand binding affinity scoring) Dataset: CASF-2016 | 0.738 Pearson R unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 scoring Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 3: CASF-2016 scoring Pearson R |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 ranking (Protein–ligand binding affinity scoring) Dataset: CASF-2016 ranking | 0.539 Spearman correlation unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 ranking Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 4: CASF-2016 ranking Spearman correlation |
| Configuration: K DEEP · 0.0001 | Protocol: CASF-2016 docking (Protein–ligand binding affinity scoring) Dataset: CASF-2016 docking | 52.2% Top 3 success percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceK DEEP · 0.0001: CASF-2016 docking Training uses 3,772 PDBbind-2016 refined-set complexes after removal of the 285-complex core test set. CASF separates scoring, ranking and docking power. Aggregation: Not reported AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 9: CASF-2016 docking Top 3 success |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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Evaluation in this paper
K_DEEP reimplemented by AK-score authors in Keras 2.2.4 / TensorFlow 1.13.1; Table-specific network configuration; learning rate 0.0001
Sources
AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAEStrengths, limitations and unresolved questions
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Stable record: paper-model-23f232fc26d8880fb1Specifications
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Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
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|---|---|
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper K_DEEP reimplemented by AK-score authors in Keras 2.2.4 / TensorFlow 1.13.1; Table-specific network configuration; learning rate 0.0001 Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAE Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Introduction K DEEP as evaluated in the cited study. K_DEEP reimplemented by AK-score authors in Keras 2.2.4 / TensorFlow 1.13.1; Table-specific network configuration; learning rate 0.0001 Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAE Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-29-06401fd5b220 · Record review: needs review
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- AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Original source · version of record
Technical metadata and extraction receipts
Stable ID: paper-model-23f232fc26d8880fb1
- areas
- molecular-interactions
- tasks
- Protein–ligand binding affinity scoring
- entity level
- method
- configuration type
- reported_configuration
- version
- K_DEEP reimplemented by AK-score authors in Keras 2.2.4 / TensorFlow 1.13.1; Table-specific network configuration; learning rate 0.0001
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: akscore-2020; source locator: Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAE; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.