Datasets
Kd-labelled complexes from PDBbind v2019, with the corresponding CASF-2016 core structures reserved as the external test subset.
Task
Protein–ligand binding energy prediction
Protein–ligand energy prediction compares alternative fingerprint descriptors and regression methods.
Sources
Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61Overview
Metrics
Pearson correlation and root-mean-square error.
Sources
Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61Allowed inputs
Protein/ligand fingerprint combinations.
Sources
Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: PMF + ECFP + PF (LightGBM) | Task: Protein–ligand binding energy prediction Dataset: Fingerprint-scoring benchmark | 0.79 Pearson R unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePMF + ECFP + PF (LightGBM): Protein–ligand binding energy prediction Binding-energy model using ligand and protein fingerprints with LightGBM. Aggregation: Not reported Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Table 1, PMF + ECFP + PF / LightGBM row, R column |
| Configuration: PMF (LASSO) | Task: Protein–ligand binding energy prediction Dataset: Fingerprint-scoring benchmark | 0.67 Pearson R unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePMF (LASSO): Protein–ligand binding energy prediction PMF-only LASSO baseline evaluated by the same authors. Aggregation: Not reported Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Table 1, PMF / LASSO row, R column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
Kd-labelled complexes from PDBbind v2019, with the corresponding CASF-2016 core structures reserved as the external test subset. Pearson correlation and root-mean-square error. LASSO and LightGBM with alternative protein/ligand fingerprint combinations.
Sources
Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Computational Details, cached paragraph 30; Results and Discussion; Conclusion; cached text lines 44–46, 61; Results and Discussion; Conclusion; cached text lines 44–46, 61Recorded evaluations
Each evaluation records what was tested and under which conditions.
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- The external CASF subset separates evaluation structures from fitted examples, but the described split is not a protein-family- or ligand-scaffold-disjoint test.
Sources
Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61
Profile review details
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-94802534b7026dSpecifications
Inputs, training, access and other details
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 | Kd-labelled complexes from PDBbind v2019, with the corresponding CASF-2016 core structures reserved as the external test subset.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Computational Details, cached paragraph 30 |
| Splits | Kd-labelled PDBbind v2019 complexes are divided into training, hyperparameter-selection (“pretest”) and an external CASF-2016 core test subset. Ten random training/pretest allocations are assessed, and the allocation with correlation closest to their average is retained; the external test set is not used for fitting.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Computational Details; cached paragraphs 30–35 |
| Metrics | Pearson correlation and root-mean-square error.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Baselines | LASSO and LightGBM with alternative protein/ligand fingerprint combinations.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Leakage controls | The checked fingerprint-comparison passages do not define scaffold- or protein-target-disjoint evaluation. · Not reported in inspected sourcesSourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Entity type | Paper-specific computational evaluation protocol.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Organisms | PDBbind v2019 complexes with Kd measurements are selected for binding-energy assessment. Computational Details does not tabulate their source organisms or a species-specific evaluation subset. · Not reported in inspected sourcesSourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Computational Details, dataset selection and external CASF test |
| Assays | Protein–ligand binding-energy labels.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Allowed inputs | Protein/ligand fingerprint combinations.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
| Adaptation | Supervised regression using LASSO or LightGBM.SourcesMachine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Results and Discussion; Conclusion; cached text lines 44–46, 61 |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints | PMC archival version PMC9178954.1 | Read source DOI: 10.1021/acsomega.2c02822 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 2 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- RMSE is lower-is-better; do not mix correlation and energy errors.
- Conventional-function rows must retain software suffixes and scoring settings; exact common test/context needs methods review before merging Tables 1–2 into one chart.
Search and extraction details
primary comparison table screened
Searches
- "PMC9178954"
Evidence locations
- Tables 1–2
- Results: scoring functions
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.
17 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 | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | 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
| Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | 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 | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | 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 Kd-labelled complexes from PDBbind v2019, with the corresponding CASF-2016 core structures reserved as the external test subset. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Computational Details, cached paragraph 30 Version: PMC archival version PMC9178954.1 | 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 Kd-labelled PDBbind v2019 complexes are divided into training, hyperparameter-selection (“pretest”) and an external CASF-2016 core test subset. Ten random training/pretest allocations are assessed, and the allocation with correlation closest to their average is retained; the external test set is not used for fitting. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Computational Details; cached paragraphs 30–35 Version: PMC archival version PMC9178954.1 | 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 regression using LASSO or LightGBM. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | 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 and root-mean-square error. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | 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 LASSO and LightGBM with alternative protein/ligand fingerprint combinations. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | 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 The checked fingerprint-comparison passages do not define scaffold- or protein-target-disjoint evaluation. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | unreported 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 cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints Results and Discussion; Conclusion; cached text lines 44–46, 61 Version: PMC archival version PMC9178954.1 | unreported 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 |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Original source · PMC archival version PMC9178954.1
- Machine-Learning- and Knowledge-Based Scoring Functions Incorporating Ligand and Protein Fingerprints · Original source · PMC archival version PMC9178954.1
Technical metadata and extraction receipts
Stable ID: reported-task-94802534b7026d
- areas
- molecular-interactions
- tasks
- Protein–ligand binding energy prediction
- entity level
- task
- version
- Not reported
- task
- Protein–ligand binding energy prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_table_screened; primary sources: expansion-p3-fingerprint-scoring-2022; inspected locators: Tables 1–2; Results: scoring functions; searched queries: "PMC9178954"; gaps: RMSE is lower-is-better; do not mix correlation and energy errors.; Conventional-function rows must retain software suffixes and scoring settings; exact common test/context needs methods review before merging Tables 1–2 into one chart.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: fingerprint-scoring-2022; source locator: Results and Discussion; Conclusion; cached text lines 44–46, 61; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.