Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
Physically valid protein–ligand pose selection
Docking algorithm selection is evaluated as a workflow-dependent choice among a fixed solver portfolio.
Sources
Molecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results tableAt a glance
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 | A curated BindingMOAD-derived set and additional docking benchmarks.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Splits | Curated subset construction excludes overlap using rules independent of docking scores and solver rankings.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Metrics | PoseBusters-validity-gated pose agreement forms the workflow-specific success score; solver ranking depends on this combined criterion.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Baselines | A portfolio of eight docking algorithms is evaluated; it is explicitly not claimed to be exhaustive.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Leakage controls | The data-curation procedure is designed to reduce overlap with common PDBbind training corpora.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Uncertainty | In-domain metrics are means over five folds. Table 3 marks paired significance tests against the single-best solver, while the cross-benchmark discussion explicitly distinguishes marginal, nonsignificant gains. The score-margin diagnostics are benchmark-dependent confidence proxies, not calibrated success probabilities.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Evaluation regimes; Table 3 and footnote; In-domain learning; Fig.4 and Cross-benchmark generalisation |
| Entity type | Paper-specific computational evaluation protocol.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Organisms | MOAD-curated is selected from BindingMOAD by complex quality and overlap exclusions, alongside separate docking benchmarks. The dataset-construction section does not enumerate organisms or specify a species-conditioned evaluation. · Not reported in inspected sourcesSourcesMolecular embedding-based algorithm selection in protein-ligand docking · Dataset construction: MOAD-curated, PoseX and PoseBusters |
| Assays | Protein–ligand structures with physical-validity and reference-pose checks.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Allowed inputs | Candidate docking poses and protein–ligand complexes.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
| Adaptation | Selection/ranking among poses from a docking-method portfolio; subset construction is independent of scores.SourcesMolecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
Molecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results tableEvaluation methodology
A curated BindingMOAD-derived set and additional docking benchmarks. Curated subset construction excludes overlap using rules independent of docking scores and solver rankings. PoseBusters-validity-gated pose agreement forms the workflow-specific success score; solver ranking depends on this combined criterion. A portfolio of eight docking algorithms is evaluated; it is explicitly not claimed to be exhaustive. The data-curation procedure is designed to reduce overlap with common PDBbind training corpora.
Sources
Molecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results tableRecorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| MolAS: Physically valid protein–ligand pose selection Averaged five-fold algorithm-selection performance on PoseBusters; joint RMSD and validity criterion. Author-reported evaluation · Evaluation metadata: needs review | ||
| 36.69 RMSD ≤1 Å and PB-valid success Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedMolecular embedding-based algorithm selection in protein-ligand docking · Table 3, PoseBusters / Mixed / AutoDock row, MolAS success column Source checking is not independent reproduction. |
| Single best solver: Physically valid protein–ligand pose selection Configuration: Single best solverTask: Physically valid protein–ligand pose selectionDataset: PoseBusters Single best solver baseline under the same averaged five-fold selection test. Independent external evaluation · Evaluation metadata: needs review | ||
| 34.34 RMSD ≤1 Å and PB-valid success Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedMolecular embedding-based algorithm selection in protein-ligand docking · Table 3, PoseBusters / Mixed / AutoDock row, SBS success column Source checking is not independent reproduction. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Molecular embedding-based algorithm selection in protein-ligand docking | PMC archival version PMC13104262.1 | Read source DOI: 10.1186/s13321-026-01168-8 |
What is still missing
- Complete raw table acquired. Source compares selected algorithm versusSBS percohort; gap is derived difference, not new model score. Five-fold means and paired-significance stars do not imply confidence intervals. Structured extraction pending.
Search and extraction details
source found structured extraction pending
Searches
- Molecular embedding-based algorithm selection in protein-ligand docking primary paper benchmark results
Evidence locations
- Table3,≤1Å/≤2Å PoseBusters-valid success; mixed/separate cohorts
Strengths and limitations
Limitations and conditions
- Solver rankings and oracle labels depend on benchmark and post-processing. Confidence margins are not uniformly reliable indicators of improvement over the single-best solver.
Sources
Molecular embedding-based algorithm selection in protein-ligand docking · Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table
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-d1c46526c39983Evidence 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 | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 ["Input: Candidate docking poses and protein–ligand complexes.","Evaluation: Selection/ranking among poses from a docking-method portfolio; subset construction is independent of scores.","Readout: PoseBusters-validity-gated pose agreement forms the workflow-specific success score; solver ranking depends on this combined criterion."] Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 A curated BindingMOAD-derived set and additional docking benchmarks. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 Curated subset construction excludes overlap using rules independent of docking scores and solver rankings. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 Selection/ranking among poses from a docking-method portfolio; subset construction is independent of scores. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 PoseBusters-validity-gated pose agreement forms the workflow-specific success score; solver ranking depends on this combined criterion. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 A portfolio of eight docking algorithms is evaluated; it is explicitly not claimed to be exhaustive. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 data-curation procedure is designed to reduce overlap with common PDBbind training corpora. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table Version: PMC archival version PMC13104262.1 | 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 |
| Uncertainty In-domain metrics are means over five folds. Table 3 marks paired significance tests against the single-best solver, while the cross-benchmark discussion explicitly distinguishes marginal, nonsignificant gains. The score-margin diagnostics are benchmark-dependent confidence proxies, not calibrated success probabilities. Individual claims | Molecular embedding-based algorithm selection in protein-ligand docking Evaluation regimes; Table 3 and footnote; In-domain learning; Fig.4 and Cross-benchmark generalisation Version: PMC archival version PMC13104262.1 | 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 |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- Molecular embedding-based algorithm selection in protein-ligand docking · Original source · PMC archival version PMC13104262.1
- Molecular embedding-based algorithm selection in protein-ligand docking · Original source · PMC archival version PMC13104262.1
Technical metadata and extraction receipts
Stable ID: reported-task-d1c46526c39983
- areas
- molecular-interactions
- tasks
- Physically valid protein–ligand pose selection
- entity level
- task
- version
- Not reported
- task
- Physically valid protein–ligand pose selection
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-molas-2026-d556d47e0f7b; inspected locators: Table3,≤1Å/≤2Å PoseBusters-valid success; mixed/separate cohorts; searched queries: Molecular embedding-based algorithm selection in protein-ligand docking primary paper benchmark results; gaps: Complete raw table acquired. Source compares selected algorithm versusSBS percohort; gap is derived difference, not new model score. Five-fold means and paired-significance stars do not imply confidence intervals. Structured extraction pending.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- 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: molas-2026; source locator: Methods: Datasets and preprocessing; Results framing; cached text lines 5, 9, 18–21; task metric definitions and corresponding results table; 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.