Model type
Molecular docking model; this record is the paper-specific evaluated configuration.
Configuration
DiffDock 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/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4)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 |
|---|---|---|
| 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. |
How it works
How the evaluated method works
DiffDock docks once to each protein conformation with default parameters. The trained confidence-model output supplies the pose score, which is min–max normalised within the method/ensemble setting.
Sources
Ensemble docking for intrinsically disordered proteins · Methods/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4)Underlying method and version boundaries
DiffDock is a molecular-docking implementation that produces ligand poses and confidence estimates. Its confidence values and predicted coordinates are different outputs from an experimentally calibrated binding-affinity measurement.
Sources
gcorso/DiffDock README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies DiffDock 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-b3-047Strengths 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-75e4e5e5965320Specifications
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 | Molecular docking model; this record is the paper-specific evaluated configuration.Sourcesgcorso/DiffDock README.md · README.md model description |
| Architecture / procedure | DiffDock docks once to each protein conformation with default parameters. The trained confidence-model output supplies the pose score, which is min–max normalised within the method/ensemble setting.SourcesEnsemble docking for intrinsically disordered proteins · Methods/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4) |
| 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 | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Ensemble docking for intrinsically disordered proteins; gcorso/DiffDock README.md · Methods/MD Simulations.; Methods/t-SNE clustering.; Methods/AutoDock Vina ensemble docking.; Methods/DiffDock Ensemble docking.; Methods/Analysis of IDP ligand binding modes.; Methods/Docked-pose RMSD calculations.; Methods/Comparing docking scores.; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | DiffDock 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 | The pretrained docking model is evaluated on holo conformations from the study’s ligand-bound molecular-dynamics ensemble; no affinity-label fine-tuning is described.SourcesEnsemble docking for intrinsically disordered proteins · Results/Quantifying the similarity of ligand binding poses obtained from MD simulations and ensemble docking. (paragraph 4); Methods/t-SNE clustering. (paragraph 1) |
| Context limits | The evaluated receptor ensemble is the 20-residue α-synuclein C-terminal fragment 121–140; this study-specific input is not a general DiffDock context maximum.SourcesEnsemble docking for intrinsically disordered proteins · Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 1); Results/Ensemble docking accurately predicts the relative affinities of small molecules to α-synuclein. (paragraph 1) |
| Access | Official upstream implementation and usage documentation: https://github.com/gcorso/DiffDock/blob/85c49b60d3e0b0182a59ee43a34a6d7036981284/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesgcorso/DiffDock README.md · README.md; installation, model download and usage instructions |
| Code licence | MIT (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesgcorso/DiffDock LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesgcorso/DiffDock README.md · README.md; checkpoint/access documentation and licence scope |
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.
21 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/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4) 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","DiffDock holo","Docked poses and normalised relative docking scores"] Individual claims | Ensemble docking for intrinsically disordered proteins Methods/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4) 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/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4) 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 Molecular docking model; this record is the paper-specific evaluated configuration. Individual claims | gcorso/DiffDock README.md README.md model description Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | 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 DiffDock docks once to each protein conformation with default parameters. The trained confidence-model output supplies the pose score, which is min–max normalised within the method/ensemble setting. Individual claims | Ensemble docking for intrinsically disordered proteins Methods/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4) 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 The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | gcorso/DiffDock README.md README.md; checkpoint/access documentation and licence scope Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | 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 |
| 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 An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | Ensemble docking for intrinsically disordered proteins Methods/MD Simulations.; Methods/t-SNE clustering.; Methods/AutoDock Vina ensemble docking.; Methods/DiffDock Ensemble docking.; Methods/Analysis of IDP ligand binding modes.; Methods/Docked-pose RMSD calculations.; Methods/Comparing docking scores.; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. 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 |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | gcorso/DiffDock README.md Methods/MD Simulations.; Methods/t-SNE clustering.; Methods/AutoDock Vina ensemble docking.; Methods/DiffDock Ensemble docking.; Methods/Analysis of IDP ligand binding modes.; Methods/Docked-pose RMSD calculations.; Methods/Comparing docking scores.; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | 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
- gcorso/DiffDock README.md · Original source · 85c49b60d3e0b0182a59ee43a34a6d7036981284
- gcorso/DiffDock LICENSE · Original source · 85c49b60d3e0b0182a59ee43a34a6d7036981284
Technical metadata and extraction receipts
Stable ID: reported-model-75e4e5e5965320
- areas
- molecular-interactions
- entity level
- method
- version
- Not reported
- reported name
- DiffDock 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-diffdock-readme-md; source locator: Methods/DiffDock Ensemble docking. (paragraph 1); Results/Ensemble docking protocols for intrinsically disordered proteins. (paragraph 4) | 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.