Protocol

CASF-2016 docking (Protein–ligand binding affinity scoring)

CASF-2016 docking · Top 1 success. 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.

AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks · A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success

9 evaluations · 27 metric rows

At 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

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.

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Tasks

Protein–ligand binding affinity scoring

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

CASF-2016 docking · Top 1 success

Top 1 success (percent) · Higher 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.

Evaluation protocol · CASF-2016 docking

K DEEP · 0.0001 · Configuration · Independent external evaluation24.8
K DEEP · 0.0005 · Configuration · Independent external evaluation29.1
K DEEP · 0.0006 · Configuration · Independent external evaluation29.1
K DEEP · 0.0010 · Configuration · Independent external evaluation24.8
AK-score-single · 0.0001 · Configuration · Author-reported evaluation34.9
AK-score-single · 0.0005 · Configuration · Author-reported evaluation29.9
AK-score-single · 0.0007 · Configuration · Author-reported evaluation31.3
AK-score-single · 0.0010 · Configuration · Author-reported evaluation26.3
AK-score-ensemble · 0.0007 · Configuration · Author-reported evaluation 36.0

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.

Values, uncertainty and evidence

Top 1 success: original source values
Tested entity	Printed value	Uncertainty	Evidence
K DEEP · 0.0001 · Configuration	24.8 percent	Not reported	Independent external evaluation · source checkedAK-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
K DEEP · 0.0005 · Configuration	29.1 percent	Not reported	Independent external evaluation · 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
K DEEP · 0.0006 · Configuration	29.1 percent	Not reported	Independent external evaluation · 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 7: CASF-2016 docking Top 1 success
K DEEP · 0.0010 · Configuration	24.8 percent	Not reported	Independent external evaluation · 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
AK-score-single · 0.0001 · Configuration	34.9 percent	Not reported	Author-reported evaluation · 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
AK-score-single · 0.0005 · Configuration	29.9 percent	Not reported	Author-reported evaluation · 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
AK-score-single · 0.0007 · Configuration	31.3 percent	Not reported	Author-reported evaluation · 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
AK-score-single · 0.0010 · Configuration	26.3 percent	Not reported	Author-reported evaluation · 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 7: CASF-2016 docking Top 1 success
AK-score-ensemble · 0.0007 · Configuration	36.0 percent	Not reported	Author-reported evaluation · 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 7: CASF-2016 docking Top 1 success

Scope and limitations

Learning rates define distinct evaluated configurations. Table 2 ensemble Pearson 0.812 is distinct from the 30-network ensemble Pearson 0.827 in Figure 3. Do not transfer the 285-complex scoring denominator to ranking or docking rows without their appropriate grouping. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 9 evaluations · 27 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
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.
36.3% 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 6 K DEEP, column 8: CASF-2016 docking Top 2 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.
56.1% 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 7 AK-score-single, column 9: CASF-2016 docking Top 3 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.
36.0 % 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 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction.
51.4 % 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 11 AK-score-ensemble, column 8: CASF-2016 docking Top 2 success 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.
54.0% 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 8 AK-score-single, column 9: CASF-2016 docking Top 3 success Source checking is not independent reproduction.
43.2% 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 8 AK-score-single, column 8: CASF-2016 docking Top 2 success 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.
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.
26.3% 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 10 AK-score-single, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction.
54.0% 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 10 AK-score-single, column 9: CASF-2016 docking Top 3 success Source checking is not independent reproduction.
K DEEP · 0.0001: CASF-2016 docking Configuration: K DEEP · 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. Independent external evaluation · Evaluation metadata: needs review
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 3 K DEEP, column 7: CASF-2016 docking Top 1 success Source checking is not independent reproduction.
38.5% 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 3 K DEEP, column 8: CASF-2016 docking Top 2 success Source checking is not independent reproduction.
K DEEP · 0.0006: CASF-2016 docking Configuration: K DEEP · 0.0006Protocol: 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 5 K DEEP, column 9: CASF-2016 docking Top 3 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 5 K DEEP, column 8: CASF-2016 docking Top 2 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 5 K DEEP, column 7: CASF-2016 docking Top 1 success 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.

Papers and result coverage

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 DOI: 10.3390/ijms21228424

What is still missing

exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.

Search and extraction details

complete tables extracted

Searches

AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks 10.3390/ijms21228424

Evidence locations

A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-protocol-9e3344661a0f282e5e

Evidence 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.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Evaluation in this paper 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. Individual claims	AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Original source ↗ A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success Version: version of record Retrieved: 2026-09-16T10:44:03.436853+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `40cfd28dcd587599768ec99a6590ec593486475ff01c7b1d1f229b44aa91bf8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Introduction CASF-2016 docking · Top 1 success. 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. Individual claims	AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Original source ↗ A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success Version: version of record Retrieved: 2026-09-16T10:44:03.436853+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `40cfd28dcd587599768ec99a6590ec593486475ff01c7b1d1f229b44aa91bf8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: evaluates task reported-task-a78312d5df6dad Individual claims	AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Original source ↗ A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success Version: version of record Retrieved: 2026-09-16T10:44:03.436853+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-a78312d5df6dad` Claim: paper-claim-4a2ca7312f1b4d72f8 Source artifact SHA-256: `40cfd28dcd587599768ec99a6590ec593486475ff01c7b1d1f229b44aa91bf8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

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

Download this release

Technical metadata and extraction receipts

Stable ID: paper-protocol-9e3344661a0f282e5e

areas: molecular-interactions
tasks: Protein–ligand binding affinity scoring
entity level: protocol
protocol: 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.
comparison panels: id: akscore-2020-ijms-21-08424-t002-top1; title: CASF-2016 docking · Top 1 success; protocol id: paper-protocol-9e3344661a0f282e5e; dataset id: paper-dataset-30865ab989a9b4a55d; metric: Top 1 success; unit: percent; direction: higher; result ids: paper-result-3c9458f5230898c118; paper-result-b621ddd15cd16afefc; paper-result-c7f5dc9eb4c9ae58e6; paper-result-1aebc62b50d2a564cb; paper-result-045168c33da4f91423; paper-result-11080ec943cd58cc49; paper-result-2bb9d0ff2467197946; paper-result-76f65e01a22812dc8f; paper-result-9d866f174829993930; source ids: akscore-2020; source locator: A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success; context: 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.; caveats: Learning rates define distinct evaluated configurations. Table 2 ensemble Pearson 0.812 is distinct from the 30-network ensemble Pearson 0.827 in Figure 3. Do not transfer the 285-complex scoring denominator to ranking or docking rows without their appropriate grouping. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: akscore-2020-ijms-21-08424-t002-top2; title: CASF-2016 docking · Top 2 success; protocol id: paper-protocol-9e3344661a0f282e5e; dataset id: paper-dataset-30865ab989a9b4a55d; metric: Top 2 success; unit: percent; direction: higher; result ids: paper-result-696ea3d9b8dda19fd4; paper-result-e74ffc4f5d72ad3621; paper-result-6723f12f371db71f52; paper-result-928b3ac5d356652219; paper-result-ed9c485f143578778f; paper-result-97d06bfff5bd0deec7; paper-result-2257bde111aae5f357; paper-result-2aad15d58eda971fd3; paper-result-d88b7ac6133e0902be; source ids: akscore-2020; source locator: A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 8: CASF-2016 docking Top 2 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 8: CASF-2016 docking Top 2 success; context: 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.; caveats: Learning rates define distinct evaluated configurations. Table 2 ensemble Pearson 0.812 is distinct from the 30-network ensemble Pearson 0.827 in Figure 3. Do not transfer the 285-complex scoring denominator to ranking or docking rows without their appropriate grouping. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: akscore-2020-ijms-21-08424-t002-top3; title: CASF-2016 docking · Top 3 success; protocol id: paper-protocol-9e3344661a0f282e5e; dataset id: paper-dataset-30865ab989a9b4a55d; metric: Top 3 success; unit: percent; direction: higher; result ids: paper-result-f70d87df9407fc2486; paper-result-b4bea686f5bbd1459b; paper-result-5b72ab3d9513410a5f; paper-result-031247a72fb2604f0e; paper-result-7d7b1a31163a7d9b6b; paper-result-79f7e7e650d400e1bf; paper-result-1f1a756aa0ab1e0734; paper-result-e3010fc8650e08fdd7; paper-result-08702d09e3ca13e618; source ids: akscore-2020; source locator: A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 9: CASF-2016 docking Top 3 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 9: CASF-2016 docking Top 3 success; context: 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.; caveats: Learning rates define distinct evaluated configurations. Table 2 ensemble Pearson 0.812 is distinct from the 30-network ensemble Pearson 0.827 in Figure 3. Do not transfer the 285-complex scoring denominator to ranking or docking rows without their appropriate grouping. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_tables_extracted; primary sources: akscore-2020; inspected locators: A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success; searched queries: AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks 10.3390/ijms21228424; gaps: exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: 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.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: akscore-2020; source locator: A comparison of prediction accuracy with the CASF-2016 dataset.; Table 2 (ijms-21-08424-t002), row 3 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 7: CASF-2016 docking Top 1 success; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 7: CASF-2016 docking Top 1 success; ambiguities: None recorded

Related records

evaluates task: Protein–ligand binding affinity scoring
subject: CASF-2016 docking (Protein–ligand binding affinity scoring): links:evaluates_task:reported-task-a78312d5df6dad
benchmark: AK-score-single · 0.0010: CASF-2016 docking
benchmark: AK-score-single · 0.0007: CASF-2016 docking
benchmark: K DEEP · 0.0001: CASF-2016 docking
benchmark: K DEEP · 0.0010: CASF-2016 docking
benchmark: AK-score-ensemble · 0.0007: CASF-2016 docking
benchmark: AK-score-single · 0.0005: CASF-2016 docking
benchmark: K DEEP · 0.0005: CASF-2016 docking
benchmark: AK-score-single · 0.0001: CASF-2016 docking
benchmark: K DEEP · 0.0006: CASF-2016 docking

Suggest a correction