Protocol

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

CASF-2016 ranking · Spearman correlation. 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.

Sources

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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation

9 evaluations · 27 metric rows

At a glance

Inputs, training, access and other details

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.

Data, procedure and scoring
Property	Description and evidence
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Splits	Not extracted or verified for this record.
Allowed inputs	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Metrics	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

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.

Sources

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 ranking · Spearman correlation

Spearman correlation (unitless) · 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 ranking

K DEEP · 0.0001 · Configuration · Independent external evaluation0.539
K DEEP · 0.0005 · Configuration · Independent external evaluation0.486
K DEEP · 0.0006 · Configuration · Independent external evaluation0.528
K DEEP · 0.0010 · Configuration · Independent external evaluation0.479
AK-score-single · 0.0001 · Configuration · Author-reported evaluation0.572
AK-score-single · 0.0005 · Configuration · Author-reported evaluation0.596
AK-score-single · 0.0007 · Configuration · Author-reported evaluation0.616
AK-score-single · 0.0010 · Configuration · Author-reported evaluation0.598
AK-score-ensemble · 0.0007 · Configuration · Author-reported evaluation 0.670

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

Spearman correlation: original source values
Tested entity	Printed value	Uncertainty	Evidence
K DEEP · 0.0001 · Configuration	0.539 unitless	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 4: CASF-2016 ranking Spearman correlation
K DEEP · 0.0005 · Configuration	0.486 unitless	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 4: CASF-2016 ranking Spearman correlation
K DEEP · 0.0006 · Configuration	0.528 unitless	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 4: CASF-2016 ranking Spearman correlation
K DEEP · 0.0010 · Configuration	0.479 unitless	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 4: CASF-2016 ranking Spearman correlation
AK-score-single · 0.0001 · Configuration	0.572 unitless	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 4: CASF-2016 ranking Spearman correlation
AK-score-single · 0.0005 · Configuration	0.596 unitless	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 4: CASF-2016 ranking Spearman correlation
AK-score-single · 0.0007 · Configuration	0.616 unitless	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 4: CASF-2016 ranking Spearman correlation
AK-score-single · 0.0010 · Configuration	0.598 unitless	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 4: CASF-2016 ranking Spearman correlation
AK-score-ensemble · 0.0007 · Configuration	0.670 unitless	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 4: CASF-2016 ranking Spearman correlation

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
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.
0.670 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 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation 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.
0.598 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 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation 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.
0.439 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 5 K DEEP, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction.
0.528 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 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation Source checking is not independent reproduction.
AK-score-single · 0.0007: CASF-2016 ranking Configuration: AK-score-single · 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
0.640 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 9 AK-score-single, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction.
0.616 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 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation Source checking is not independent reproduction.
0.526 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 9 AK-score-single, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction.
AK-score-single · 0.0005: CASF-2016 ranking Configuration: AK-score-single · 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. Author-reported evaluation · Evaluation metadata: needs review
0.512 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 8 AK-score-single, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction.
0.616 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 8 AK-score-single, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction.
K DEEP · 0.0010: CASF-2016 ranking Configuration: K DEEP · 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. Independent external evaluation · Evaluation metadata: needs review
0.492 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 6 K DEEP, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction.
0.479 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 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation Source checking is not independent reproduction.
0.400 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 6 K DEEP, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction.
K DEEP · 0.0001: CASF-2016 ranking Configuration: K DEEP · 0.0001Protocol: 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
0.559 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 3 K DEEP, column 6: CASF-2016 ranking Predictive Index Source checking is not independent reproduction.
0.435 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 3 K DEEP, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction.
0.539 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 3 K DEEP, column 4: CASF-2016 ranking Spearman correlation 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.
AK-score-single · 0.0001: CASF-2016 ranking Configuration: AK-score-single · 0.0001Protocol: 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
0.456 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 7 AK-score-single, column 5: CASF-2016 ranking Kendall tau Source checking is not independent reproduction.
0.572 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 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation Source checking is not independent reproduction.
0.600 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 7 AK-score-single, column 6: CASF-2016 ranking Predictive Index 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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation

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-0c5a1c5ef6896a2d96

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation 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 ranking · Spearman correlation. 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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation 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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation 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-44afb78999a73a20ae Source artifact SHA-256: `40cfd28dcd587599768ec99a6590ec593486475ff01c7b1d1f229b44aa91bf8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-09-17-d277315f7d76 · 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

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Technical metadata and extraction receipts

Stable ID: paper-protocol-0c5a1c5ef6896a2d96

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-spearman; title: CASF-2016 ranking · Spearman correlation; protocol id: paper-protocol-0c5a1c5ef6896a2d96; dataset id: paper-dataset-1586129df956852448; metric: Spearman correlation; unit: unitless; direction: higher; result ids: paper-result-afde916d0d344fa5f3; paper-result-ed6bcd67134333f58a; paper-result-ebaae58e746eec83a7; paper-result-b2042668888da9601a; paper-result-ce979d714ded7834b1; paper-result-fcef1022a440b405a6; paper-result-85878ef679c27f7b5c; paper-result-e0b7d3b3917b02dad0; paper-result-7ea147a4415e34f1f0; 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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation; 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-kendall; title: CASF-2016 ranking · Kendall tau; protocol id: paper-protocol-0c5a1c5ef6896a2d96; dataset id: paper-dataset-1586129df956852448; metric: Kendall tau; unit: unitless; direction: higher; result ids: paper-result-7efbb2fd6cff6823e3; paper-result-6a2d74d436874496a7; paper-result-a1a3952f6bd9e2b283; paper-result-bb8ec19b9079636bfc; paper-result-c259bffd41e1648664; paper-result-5505231aa7e1d37837; paper-result-955fc84c22143025f1; paper-result-2eed37f01d919cd0e6; paper-result-38d90f85618bbf9bbb; 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 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 5: CASF-2016 ranking Kendall tau; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 5: CASF-2016 ranking Kendall tau; 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-pi; title: CASF-2016 ranking · Predictive Index; protocol id: paper-protocol-0c5a1c5ef6896a2d96; dataset id: paper-dataset-1586129df956852448; metric: Predictive Index; unit: unitless; direction: higher; result ids: paper-result-5bc9b7cb53278a9249; paper-result-b1bed56b343f3c834f; paper-result-38ac6df2e198d58359; paper-result-5a60e66ec1c7bcaf4c; paper-result-e05720b0b94095d5af; paper-result-85c6bc19be77938986; paper-result-3d0c6443af15768910; paper-result-35759619206bf32ae8; paper-result-0d44e20dd3c089c7f3; 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 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 6: CASF-2016 ranking Predictive Index; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 6: CASF-2016 ranking Predictive Index; 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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation; 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 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 4 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 5 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 6 K DEEP, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 7 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 8 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 9 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 10 AK-score-single, column 4: CASF-2016 ranking Spearman correlation; Table 2 (ijms-21-08424-t002), row 11 AK-score-ensemble, column 4: CASF-2016 ranking Spearman correlation; ambiguities: None recorded

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

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