Model type
Empirical docking algorithm; this record is the paper-specific evaluated configuration.
Configuration
AutoDock Vina holo
This holo-ensemble docking configuration evaluates small-molecule binding to α-synuclein conformations.
Sources
Ensemble docking for intrinsically disordered proteins · Discussion (paragraph 7); Introduction (paragraph 6)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Ensemble docking for intrinsically disordered proteins · Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1)At a glance
Biological inputs
Ligands and holo protein conformations from the study’s molecular-dynamics ensemble
Sources
Ensemble docking for intrinsically disordered proteins · Introduction (paragraph 4); Methods/Docked-pose RMSD calculations. (paragraph 2)Outputs
Docked poses and normalised relative docking scores
Sources
Ensemble docking for intrinsically disordered proteins · Results (paragraph 3); Results/Ensemble docking accurately predicts the relative affinities of small molecules to α-synuclein. (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. 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. |
How it works
How the evaluated method works
For each holo α-synuclein conformation, Vina docks at each residue with rigid side chains and ligand torsional freedom. The best-scoring pose is retained, then scores are min–max normalised within the method/ensemble setting.
Sources
Ensemble docking for intrinsically disordered proteins · Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1)Underlying method and version boundaries
AutoDock Vina performs molecular docking using an empirical scoring function and an optimisation procedure. The scoring-function choice, search space and supplied receptor structure define the evaluation setting.
Sources
ccsb-scripps/AutoDock-Vina README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies AutoDock Vina holo: Intrinsically disordered protein ensemble docking. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Ensemble docking for intrinsically disordered proteins · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-046Strengths and limitations
Strengths and considerations
- Represents an intrinsically disordered target as an ensemble rather than a single rigid structure.
Sources
Ensemble docking for intrinsically disordered proteins · Abstract (paragraph 1); Introduction (paragraph 1)
Limitations and conditions
- The normalised scores have method-specific meanings and are not directly calibrated binding free energies.
Sources
Ensemble docking for intrinsically disordered proteins · Methods/Comparing docking scores. (paragraph 1); Results/Ensemble docking accurately reproduces IDP ligand binding modes observed in experimentally validated long timescale MD simulations. (paragraph 2)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-1587ab674d30a2Specifications
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 |
|---|---|
| Model type | Empirical docking algorithm; this record is the paper-specific evaluated configuration.Sourcesccsb-scripps/AutoDock-Vina README.md · README.md model description |
| Architecture / procedure | For each holo α-synuclein conformation, Vina docks at each residue with rigid side chains and ligand torsional freedom. The best-scoring pose is retained, then scores are min–max normalised within the method/ensemble setting.SourcesEnsemble docking for intrinsically disordered proteins · Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1) |
| Biological inputs | Ligands and holo protein conformations from the study’s molecular-dynamics ensembleSourcesEnsemble docking for intrinsically disordered proteins · Introduction (paragraph 4); Methods/Docked-pose RMSD calculations. (paragraph 2) |
| Outputs | Docked poses and normalised relative docking scoresSourcesEnsemble docking for intrinsically disordered proteins · Results (paragraph 3); Results/Ensemble docking accurately predicts the relative affinities of small molecules to α-synuclein. (paragraph 1) |
| Parameters | Not applicable to a neural parameter count: this is an empirical scoring and conformational search procedure. · Not applicableSourcesEnsemble docking for intrinsically disordered proteins · Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 3); Discussion (paragraph 5) |
| Known versions / configuration | AutoDock Vina holo is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesEnsemble docking for intrinsically disordered proteins · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | No task-specific neural fitting is described for this docking comparator; the scoring function and receptor/ligand preparation define the procedure.SourcesEnsemble docking for intrinsically disordered proteins · Results/Ensemble docking accurately reproduces IDP ligand binding modes observed in experimentally validated long timescale MD simulations. (paragraph 1); Methods/Comparing docking scores. (paragraph 2) |
| Context limits | Not applicable to a sequence-token limit: receptor coordinates, ligand conformers and the defined search region determine the input. · Not applicableSourcesEnsemble docking for intrinsically disordered proteins · Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4); Results/Quantifying the similarity of ligand binding poses obtained from MD simulations and ensemble docking. (paragraph 5) |
| Access | Official upstream implementation and usage documentation: https://github.com/ccsb-scripps/AutoDock-Vina/blob/3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesccsb-scripps/AutoDock-Vina README.md · README.md; installation, model download and usage instructions |
| Code licence | Apache 2.0 (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesccsb-scripps/AutoDock-Vina LICENSE · LICENSE; complete licence text |
| Weights licence | Not applicable: no pretrained neural checkpoint is used. · Not applicableSourcesEnsemble docking for intrinsically disordered proteins · Data & Code Availability (paragraph 1); Discussion (paragraph 5) |
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.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Ensemble docking for intrinsically disordered proteins Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1) Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Ligands and holo protein conformations from the study’s molecular-dynamics ensemble","AutoDock Vina holo","Docked poses and normalised relative docking scores"] Individual claims | Ensemble docking for intrinsically disordered proteins Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1) Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Ensemble docking for intrinsically disordered proteins Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1) Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Empirical docking algorithm; this record is the paper-specific evaluated configuration. Individual claims | ccsb-scripps/AutoDock-Vina README.md README.md model description Version: 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure For each holo α-synuclein conformation, Vina docks at each residue with rigid side chains and ligand torsional freedom. The best-scoring pose is retained, then scores are min–max normalised within the method/ensemble setting. Individual claims | Ensemble docking for intrinsically disordered proteins Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1) Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence Not applicable: no pretrained neural checkpoint is used. Individual claims | Ensemble docking for intrinsically disordered proteins Data & Code Availability (paragraph 1); Discussion (paragraph 5) Version: preprint archived 2025-01-26 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Ligands and holo protein conformations from the study’s molecular-dynamics ensemble Individual claims | Ensemble docking for intrinsically disordered proteins Introduction (paragraph 4); Methods/Docked-pose RMSD calculations. (paragraph 2) Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Docked poses and normalised relative docking scores Individual claims | Ensemble docking for intrinsically disordered proteins Results (paragraph 3); Results/Ensemble docking accurately predicts the relative affinities of small molecules to α-synuclein. (paragraph 1) Version: preprint archived 2025-01-26 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters Not applicable to a neural parameter count: this is an empirical scoring and conformational search procedure. Individual claims | Ensemble docking for intrinsically disordered proteins Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 3); Discussion (paragraph 5) Version: preprint archived 2025-01-26 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration AutoDock Vina holo is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Ensemble docking for intrinsically disordered proteins Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: preprint archived 2025-01-26 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. 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
3 source records and release history
- Ensemble docking for intrinsically disordered proteins · Original source · preprint archived 2025-01-26
- ccsb-scripps/AutoDock-Vina README.md · Original source · 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645
- ccsb-scripps/AutoDock-Vina LICENSE · Original source · 3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645
Technical metadata and extraction receipts
Stable ID: reported-model-1587ab674d30a2
- areas
- molecular-interactions
- entity level
- method
- version
- Not reported
- reported name
- AutoDock Vina holo
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: 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
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: ensemble-idp-docking-2025; evidence-reported-base-vina-readme-md; source locator: Methods/AutoDock Vina ensemble docking. (paragraph 1); Methods/DiffDock Ensemble docking. (paragraph 1) | README.md model description | Discussion (paragraph 7); Introduction (paragraph 6); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.