Datasets
Ligand-bound intrinsically disordered protein ensembles used as computational reference conformations.
Task
Intrinsically disordered protein ensemble docking
Ensemble docking is assessed against molecular-dynamics conformations using two distinct pose-matching definitions.
Sources
Ensemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passagesOverview
Metrics
Frame-matched ligand RMSD compares corresponding conformations; best-matched RMSD selects the closest reference conformation within a cluster.
Allowed inputs
Ligands and alternative protein conformations.
Sources
Ensemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passagesEvaluation 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
Ensemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passageslimited 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: AutoDock Vina holo | Task: Intrinsically disordered protein ensemble docking Dataset: α-synuclein Ligand 47 MD ensemble | 28 Docked frames best-matched RMSD <3 Å % · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAutoDock Vina holo: Intrinsically disordered protein ensemble docking Fraction of docked frames within 3 Å of MD-observed bound pose; holo protein ensemble. Aggregation: Not reported Ensemble docking for intrinsically disordered proteins · Table 2, Ligand 47 row, AutoDock Vina Holo Docking column |
| Configuration: DiffDock holo | Task: Intrinsically disordered protein ensemble docking Dataset: α-synuclein Ligand 47 MD ensemble | 21.3 Docked frames best-matched RMSD <3 Å % · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDiffDock holo: Intrinsically disordered protein ensemble docking Fraction of docked frames within 3 Å of MD-observed bound pose; holo protein ensemble. Aggregation: Not reported Ensemble docking for intrinsically disordered proteins · Table 2, Ligand 47 row, DiffDock Holo Docking 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
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.
Sources
Ensemble docking for intrinsically disordered proteins · Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passagesRecorded 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
- Cross-docking asks whether a method tolerates a receptor conformation associated with a different ligand.
Sources
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
Limitations and conditions
- Best-match selection is more permissive than frame-matched evaluation. These MD-referenced results are not automatically experimental pose-validation results.
Sources
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
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-dec9e0f5e3da2aSpecifications
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 | 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 |
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 |
|---|---|---|
| Ensemble docking for intrinsically disordered proteins | preprint archived 2025-01-26 | Read source DOI: 10.1101/2025.01.23.634614 |
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.
- Parenthesized numbers are the <5 Å success percentage, not uncertainty; main numbers use <3 Å.
- Each ligand and ensemble/matching definition needs its own group; do not pool them.
- MD-reference agreement is not experimental binding affinity.
Search and extraction details
primary comparison table screened
Searches
- "PMC11785235"
Evidence locations
- Tables 1–2 captions
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.
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
| 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 |
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
- Ensemble docking for intrinsically disordered proteins · Original source · preprint archived 2025-01-26
- Ensemble docking for intrinsically disordered proteins · Original source · preprint archived 2025-01-26
Technical metadata and extraction receipts
Stable ID: reported-task-dec9e0f5e3da2a
- areas
- molecular-interactions
- tasks
- Intrinsically disordered protein ensemble docking
- entity level
- task
- version
- Not reported
- task
- Intrinsically disordered protein ensemble docking
- 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-ensemble-idp-docking-2025; inspected locators: Tables 1–2 captions; searched queries: "PMC11785235"; gaps: Parenthesized numbers are the <5 Å success percentage, not uncertainty; main numbers use <3 Å.; Each ligand and ensemble/matching definition needs its own group; do not pool them.; MD-reference agreement is not experimental binding affinity.; 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: ensemble-idp-docking-2025; source locator: Results: cross docking; Methods: RMSD calculations; cached text lines 46, 54, 77–78; uncertainty/repeat-run/statistical-comparison passages; 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.