Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
K DEEP · 0.0005
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 0.0005
AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 3 K DEEP, column 3: PDBbind-2016 core set MAEAt a glance
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.
How it works
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 0.0005
AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 3 K DEEP, column 3: PDBbind-2016 core set MAEEvaluations and results
Release 2026-09-17-d277315f7d76 · 4 evaluations · 9 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| K DEEP · 0.0005: PDBbind-2016 core set Configuration: K DEEP · 0.0005Protocol: PDBbind-2016 core set (Protein–ligand binding affinity scoring)Dataset: 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 1.200 MAE Unit: kcal/mol · Direction: lower | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 3 K DEEP, column 3: PDBbind-2016 core set MAE Source checking is not independent reproduction. |
| 1.519 RMSE Unit: kcal/mol · Direction: lower | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 3 K DEEP, column 4: PDBbind-2016 core set RMSE Source checking is not independent reproduction. |
| K DEEP · 0.0005: CASF-2016 ranking Configuration: K DEEP · 0.0005Protocol: CASF-2016 ranking (Protein–ligand binding affinity scoring)Dataset: 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.389 Kendall tau Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction. |
| 0.535 Predictive Index Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction. |
| 0.486 Spearman correlation Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation Source checking is not independent reproduction. |
| K DEEP · 0.0005: CASF-2016 scoring Configuration: K DEEP · 0.0005Protocol: CASF-2016 scoring (Protein–ligand binding affinity scoring)Dataset: CASF-2016 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.709 Pearson R Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 3: CASF-2016 scoring Pearson R Source checking is not independent reproduction. |
| K DEEP · 0.0005: CASF-2016 docking Configuration: K DEEP · 0.0005Protocol: CASF-2016 docking (Protein–ligand binding affinity scoring)Dataset: 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 49.6% Top 3 success Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 9: CASF-2016 docking Top 3 success Source checking is not independent reproduction. |
| 29.1% Top 1 success Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction. |
| 39.9% Top 2 success Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 8: CASF-2016 docking Top 2 success Source checking is not independent reproduction. |
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-model-e1f4a79e227e481d4bEvidence table
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.
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 0.0005 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 3 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 0.0005 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 3 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 |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
- 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-e1f4a79e227e481d4b
- 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 0.0005
- 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 3 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.