Ensemble docking is assessed against molecular-dynamics conformations using two distinct pose-matching definitions.
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 | Ligand-bound intrinsically disordered protein ensembles used as computational reference conformations.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Splits | Cross-docking evaluates a ligand using protein conformations associated with another ligand; this is distinct from a supervised split.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Metrics | Frame-matched ligand RMSD compares corresponding conformations; best-matched RMSD selects the closest reference conformation within a cluster.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Baselines | AutoDock Vina and DiffDock.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Leakage controls | Receptor ensembles and reference binding statistics come from the same previously generated molecular-dynamics trajectories. Cross-docking changes the ligand-associated receptor ensemble, rather than defining a supervised train/test split. The inspected docking methods do not audit overlap with DiffDock’s original training structures. · Not reported in inspected sourcesSourcesEnsemble docking for intrinsically disordered proteins · Results: apo/holo/cross-docking evaluation; Methods: trajectories, conformation sampling and docking |
| Uncertainty | Normalized docking-score uncertainty uses bootstrap resampling within each docked ensemble; this is distinct from uncertainty across targets.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Entity type | Paper-specific computational evaluation protocol.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Organisms | The actual evaluation uses a C-terminal α-synuclein fragment and three ligand-associated simulation collections. Its Methods identifies the reused trajectories but does not explicitly give an organism/accession for the simulated protein; references to mouse disease models are not that metadata. · Not reported in inspected sourcesSourcesEnsemble docking for intrinsically disordered proteins · Results: α-synuclein evaluation; Methods: MD simulations; Data availability |
| Assays | Ligand-bound structural ensembles used as computational references.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Allowed inputs | Ligands and alternative protein conformations.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
| Adaptation | Cross-docking with pretrained or conventional docking algorithms; this is not a supervised dataset split.SourcesEnsemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Ligand-bound intrinsically disordered protein ensembles used as computational reference conformations. Cross-docking evaluates a ligand using protein conformations associated with another ligand; this is distinct from a supervised split. Frame-matched ligand RMSD compares corresponding conformations; best-matched RMSD selects the closest reference conformation within a cluster. AutoDock Vina and DiffDock. Normalized docking-score uncertainty uses bootstrap resampling within each docked ensemble; this is distinct from uncertainty across targets.
Each evaluation records what was tested and under which conditions.
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AutoDock Vina holo: Intrinsically disordered protein ensemble docking Configuration: AutoDock Vina holoTask: Intrinsically disordered protein ensemble dockingDataset: α-synuclein Ligand 47 MD ensemble Fraction of docked frames within 3 Å of MD-observed bound pose; holo protein ensemble. Independent external evaluation · Evaluation metadata: needs review | ||
| 27.96 Docked frames best-matched RMSD <3 Å Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedEnsemble docking for intrinsically disordered proteins · Table 2, Ligand 47 row, AutoDock Vina Holo Docking column Source checking is not independent reproduction. |
| DiffDock holo: Intrinsically disordered protein ensemble docking Configuration: DiffDock holoTask: Intrinsically disordered protein ensemble dockingDataset: α-synuclein Ligand 47 MD ensemble Fraction of docked frames within 3 Å of MD-observed bound pose; holo protein ensemble. Independent external evaluation · Evaluation metadata: needs review | ||
| 21.32 Docked frames best-matched RMSD <3 Å Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedEnsemble docking for intrinsically disordered proteins · Table 2, Ligand 47 row, DiffDock Holo Docking column Source checking is not independent reproduction. |
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 |
|---|---|---|
| Ensemble docking for intrinsically disordered proteins | preprint archived 2025-01-26 | Read source DOI: 10.1101/2025.01.23.634614 |
primary comparison table screened
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-dec9e0f5e3da2aTrace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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: Ligands and alternative protein conformations.","Evaluation: Cross-docking with pretrained or conventional docking algorithms; this is not a supervised dataset split.","Readout: Frame-matched ligand RMSD compares corresponding conformations; best-matched RMSD selects the closest reference conformation within a cluster."] Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 Ligand-bound intrinsically disordered protein ensembles used as computational reference conformations. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 Cross-docking evaluates a ligand using protein conformations associated with another ligand; this is distinct from a supervised split. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 Cross-docking with pretrained or conventional docking algorithms; this is not a supervised dataset split. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 Frame-matched ligand RMSD compares corresponding conformations; best-matched RMSD selects the closest reference conformation within a cluster. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 AutoDock Vina and DiffDock. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | 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 Receptor ensembles and reference binding statistics come from the same previously generated molecular-dynamics trajectories. Cross-docking changes the ligand-associated receptor ensemble, rather than defining a supervised train/test split. The inspected docking methods do not audit overlap with DiffDock’s original training structures. Individual claims | Ensemble docking for intrinsically disordered proteins Results: apo/holo/cross-docking evaluation; Methods: trajectories, conformation sampling and docking Version: preprint archived 2025-01-26 | 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 Normalized docking-score uncertainty uses bootstrap resampling within each docked ensemble; this is distinct from uncertainty across targets. Individual claims | Ensemble docking for intrinsically disordered proteins Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-dec9e0f5e3da2a