AK-score is evaluated as a protein–ligand scoring function using PDBbind and CASF tasks that separate scoring, ranking and pose selection.
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | PDBbind-2016 refined complexes with affinity labels; the core set supplies the principal test complexes.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Splits | The core set is excluded from the refined training set; an additional evaluation uses entries newly added in PDBbind-2018.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Metrics | Pearson correlation for scoring; Spearman, Kendall and predictive index for ranking; top-ranked pose success for docking.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Baselines | Reimplemented KDEEP, AutoDock Vina and X-score are evaluated in the paper.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Leakage controls | Exact core complexes are removed from training; protein-family or ligand-scaffold independence is not established by that exclusion.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Uncertainty | The paper describes bootstrap comparison of correlation coefficients.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Entity type | Paper-specific computational evaluation protocol.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Organisms | The benchmark selects PDBbind/CASF protein–ligand complexes by structural and affinity criteria. The dataset Methods and CASF evaluation section do not report a species-stratified inventory. · Not reported in inspected sourcesSourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods: Protein–ligand data; CASF-2016 evaluation |
| Assays | Experimentally annotated protein–ligand affinities and structural poses.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Allowed inputs | Protein–ligand complex structures.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
| Adaptation | Supervised affinity scoring fitted on the refined set after excluding core test complexes.SourcesAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
PDBbind-2016 refined complexes with affinity labels; the core set supplies the principal test complexes. The core set is excluded from the refined training set; an additional evaluation uses entries newly added in PDBbind-2018. Pearson correlation for scoring; Spearman, Kendall and predictive index for ranking; top-ranked pose success for docking. Reimplemented KDEEP, AutoDock Vina and X-score are evaluated in the paper. Exact core complexes are removed from training; protein-family or ligand-scaffold independence is not established by that exclusion. The paper describes bootstrap comparison of correlation coefficients.
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Each evaluation records what was tested and under which conditions.
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
MAE (kcal/mol) · Lower values are better for this metric.
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.
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Assessment of prediction accuracy of ResNext-ensemble, ResNext, and K DEEP using the PDBbind-2016 dataset and mean absolute error and root mean square error metrics.; Table 1 (ijms-21-08424-t001), row 2 K DEEP, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 3 K DEEP, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 4 K DEEP, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 5 K DEEP, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 6 AK-score-single, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 7 AK-score-single, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 8 AK-score-single, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 9 AK-score-single, column 3: PDBbind-2016 core set MAE; Table 1 (ijms-21-08424-t001), row 10 AK-score-ensemble, column 3: PDBbind-2016 core set MAE| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| K DEEP · 0.0001 · Configuration | 1.131 kcal/mol | Not reported | Independent external evaluation · source checkedAK-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 |
| K DEEP · 0.0005 · Configuration | 1.200 kcal/mol | Not reported | Independent external evaluation · 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 |
| K DEEP · 0.0006 · Configuration | 1.164 kcal/mol | Not reported | Independent external evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 4 K DEEP, column 3: PDBbind-2016 core set MAE |
| K DEEP · 0.0010 · Configuration | 1.219 kcal/mol | Not reported | Independent external evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 5 K DEEP, column 3: PDBbind-2016 core set MAE |
| AK-score-single · 0.0001 · Configuration | 1.159 kcal/mol | Not reported | Author-reported evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 6 AK-score-single, column 3: PDBbind-2016 core set MAE |
| AK-score-single · 0.0005 · Configuration | 1.101 kcal/mol | Not reported | Author-reported evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 7 AK-score-single, column 3: PDBbind-2016 core set MAE |
| AK-score-single · 0.0007 · Configuration | 1.130 kcal/mol | Not reported | Author-reported evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 8 AK-score-single, column 3: PDBbind-2016 core set MAE |
| AK-score-single · 0.0010 · Configuration | 1.110 kcal/mol | Not reported | Author-reported evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 9 AK-score-single, column 3: PDBbind-2016 core set MAE |
| AK-score-ensemble · 0.0007 · Configuration | 1.014 kcal/mol | Not reported | Author-reported evaluation · source checkedAK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · Table 1 (ijms-21-08424-t001), row 10 AK-score-ensemble, column 3: PDBbind-2016 core set MAE |
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Release 2026-09-17-d277315f7d76 · 37 evaluations · 82 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AK-score-ensemble: Protein–ligand binding affinity scoring Configuration: AK-score-ensembleProtocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.812 Pearson R Unit: unitless · Direction: higher | Uncertainty: not reported in legacy extract 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, AK-score-ensemble / learning rate 0.0007 row, Scoring Pearson (R) column Source checking is not independent reproduction. |
| AK-score-single: Protein–ligand binding affinity scoring CASF-2016 scoring-power evaluation. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.759 Pearson R Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract 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, AK-score-single / learning rate 0.0007 row, Scoring Pearson (R) column Source checking is not independent reproduction. |
| AK-score-single · 0.0010: PDBbind-2016 core set Configuration: AK-score-single · 0.0010Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 1.110 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 9 AK-score-single, column 3: PDBbind-2016 core set MAE Source checking is not independent reproduction. |
| K DEEP · 0.0010: CASF-2016 docking Configuration: K DEEP · 0.0010Protocol: 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 | ||
| 44.6% 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 6 K DEEP, column 9: CASF-2016 docking Top 3 success Source checking is not independent reproduction. |
| 24.8% 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 6 K DEEP, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction. |
| AK-score-single · 0.0001: CASF-2016 docking Configuration: AK-score-single · 0.0001Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 34.9% 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 7 AK-score-single, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction. |
| AK-score-ensemble · 0.0007: CASF-2016 docking Configuration: AK-score-ensemble · 0.0007Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
|
59.7
% 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 11 AK-score-ensemble, column 9: CASF-2016 docking Top 3 success Source checking is not independent reproduction. |
| 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. |
| AK-score-ensemble · 0.0007: CASF-2016 ranking Configuration: AK-score-ensemble · 0.0007Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
|
0.698
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 11 AK-score-ensemble, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction. |
|
0.589
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 11 AK-score-ensemble, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction. |
| AK-score-single · 0.0005: CASF-2016 docking Configuration: AK-score-single · 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 29.9% 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 8 AK-score-single, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction. |
| AK-score-single · 0.0005: CASF-2016 scoring Configuration: AK-score-single · 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.755 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 8 AK-score-single, column 3: CASF-2016 scoring Pearson R Source checking is not independent reproduction. |
| K DEEP · 0.0010: PDBbind-2016 core set Configuration: K DEEP · 0.0010Protocol: 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 | ||
| 1.219 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 5 K DEEP, column 3: PDBbind-2016 core set MAE Source checking is not independent reproduction. |
| AK-score-single · 0.0007: CASF-2016 docking Configuration: AK-score-single · 0.0007Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 57.9% 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 9 AK-score-single, column 9: CASF-2016 docking Top 3 success Source checking is not independent reproduction. |
| 47.1% 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 9 AK-score-single, column 8: CASF-2016 docking Top 2 success Source checking is not independent reproduction. |
| 31.3% 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 9 AK-score-single, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction. |
| K DEEP · 0.0001: PDBbind-2016 core set Configuration: K DEEP · 0.0001Protocol: 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 | ||
| 1.131 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 2 K DEEP, column 3: PDBbind-2016 core set MAE Source checking is not independent reproduction. |
| 1.462 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 2 K DEEP, column 4: PDBbind-2016 core set RMSE Source checking is not independent reproduction. |
| AK-score-single · 0.0010: CASF-2016 docking Configuration: AK-score-single · 0.0010Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 43.9% 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 10 AK-score-single, column 8: CASF-2016 docking Top 2 success Source checking is not independent reproduction. |
| AK-score-single · 0.0010: CASF-2016 ranking Configuration: AK-score-single · 0.0010Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.505 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 10 AK-score-single, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction. |
| 0.627 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 10 AK-score-single, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction. |
| AK-score-single · 0.0001: CASF-2016 scoring Configuration: AK-score-single · 0.0001Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.719 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 7 AK-score-single, column 3: CASF-2016 scoring Pearson R Source checking is not independent reproduction. |
| K DEEP · 0.0006: CASF-2016 ranking Configuration: K DEEP · 0.0006Protocol: 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 | ||
| 0.558 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 5 K DEEP, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction. |
| AK-score-single · 0.0010: CASF-2016 scoring Configuration: AK-score-single · 0.0010Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.760 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 10 AK-score-single, column 3: CASF-2016 scoring Pearson R Source checking is not independent reproduction. |
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks | version of record | Read source |
complete tables extracted
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-a78312d5df6dadTrace 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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Protein–ligand complex structures.","Evaluation: Supervised affinity scoring fitted on the refined set after excluding core test complexes.","Readout: Pearson correlation for scoring; Spearman, Kendall and predictive index for ranking; top-ranked pose success for docking."] Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets PDBbind-2016 refined complexes with affinity labels; the core set supplies the principal test complexes. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits The core set is excluded from the refined training set; an additional evaluation uses entries newly added in PDBbind-2018. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised affinity scoring fitted on the refined set after excluding core test complexes. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Pearson correlation for scoring; Spearman, Kendall and predictive index for ranking; top-ranked pose success for docking. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Reimplemented KDEEP, AutoDock Vina and X-score are evaluated in the paper. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Exact core complexes are removed from training; protein-family or ligand-scaffold independence is not established by that exclusion. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The paper describes bootstrap comparison of correlation coefficients. Individual claims | AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Methods §§3.1, 3.5; Results §2.3; Table 4; cached text lines 24, 27, 40–41, 59–63 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-a78312d5df6dad