Model type
Diffusion-based molecular docking model
Model
DiffDock-L
DiffDock-L places small-molecule ligands in protein structures using a diffusion docking model.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and LicenseHow it worksDiffDock-L workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and LicenseOverview
Inputs
Protein structure and a small-molecule ligand.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and LicenseOutputs
Candidate ligand poses and confidence scores.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and LicenseAccess
Official project documentation and implementation: https://github.com/gcorso/DiffDock
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and Licenselimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: DiffDock-L | Task: Lipid–protein binding pose Dataset: LiPP lipid–protein complexes | 46.8 Success rate, ligand all-atom RMSD <2 Å % · unknown Uncertainty: 95% CI 41.3–52.3 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · source checkedMethods, coverage and sourceDiffDock-L: Lipid–protein binding pose Top-scoring pose; all-atom lipid RMSD below 2 Å. Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, DiffDock-L row, LiPP (N=331) % Success Rate column |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Use this model
How it works, versions and access
Versions and evaluated configurations
- DiffDock-L · family
How it works
How it works
DiffDock-L places small-molecule ligands in protein structures using a diffusion docking model. Diffusion-based molecular docking; the repository defaults to DiffDock-L rather than the original DiffDock model. The documented inputs are protein structure and a small-molecule ligand. The output consists of candidate ligand poses and confidence scores.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and LicenseVersions and reproducibility
DiffDock-L released February 2024; reproducing the original DiffDock requires its historical commit. The applicable input limits require configuration-specific checking.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and LicenseStrengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- The repository provides evaluation splits and instructions for PDBBind, Binding MOAD and PoseBusters.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License
Limitations and conditions
- The authors restrict the intended use to small-molecule docking. Large ligands, large protein complexes and unbound receptor conformations require particular caution.
Sources (2)
gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License
Profile review details
Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.
Stable record: catalog-model-diffdock-lSpecifications
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 | Diffusion-based molecular docking modelSources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Architecture | Diffusion-based molecular docking; the repository defaults to DiffDock-L rather than the original DiffDock model.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Inputs | Protein structure and a small-molecule ligand.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Outputs | Candidate ligand poses and confidence scores.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Parameters | Approximately 30M in the larger score model; the confidence model is a separate component, so this is not a verified total for the complete pipeline.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Known versions | DiffDock-L released February 2024; reproducing the original DiffDock requires its historical commit.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Training data | PDBBind plus filtered pre-2019 Binding MOAD complexes from training/validation protein-domain clusters, with synthetic sidechain-as-ligand augmentation for additional pocket diversity.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Training cutoff | The added Binding MOAD complexes were released before 2019; this is a component-specific restriction, not a universal cutoff for every input resource.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Context limits | This is a protein–ligand graph model rather than a fixed text-token window. The reviewed paper and README do not establish one maximum for arbitrary receptor and ligand sizes. · Not reported in inspected sourcesSources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Weights licence | MIT; README License explicitly includes code and model weights.Sources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Access | Official project documentation and implementation: https://github.com/gcorso/DiffDockSources (2)gcorso/DiffDock: README.md; diffdockl: Primary paper PDF · DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License |
| Code licence | MITSourcesgcorso/DiffDock: LICENSE · LICENSE: licence text |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
39 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | gcorso/DiffDock: README.md DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | diffdockl: Primary paper PDF DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2402.18396v1 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Diagram steps
| gcorso/DiffDock: README.md DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Diagram steps
| diffdockl: Primary paper PDF DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2402.18396v1 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title DiffDock-L workflow Individual claims | gcorso/DiffDock: README.md DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title DiffDock-L workflow Individual claims | diffdockl: Primary paper PDF DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2402.18396v1 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Model type Diffusion-based molecular docking model Individual claims | gcorso/DiffDock: README.md DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Model type Diffusion-based molecular docking model Individual claims | diffdockl: Primary paper PDF DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2402.18396v1 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Architecture Diffusion-based molecular docking; the repository defaults to DiffDock-L rather than the original DiffDock model. Individual claims | gcorso/DiffDock: README.md DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 85c49b60d3e0b0182a59ee43a34a6d7036981284 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Architecture Diffusion-based molecular docking; the repository defaults to DiffDock-L rather than the original DiffDock model. Individual claims | diffdockl: Primary paper PDF DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2402.18396v1 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
View linked audit checks and correction history
Release 2026-09-23-2b89723c6dd9 · Record review: discovered
4 source records and release history
- DiffDock-L official resource · Original source · Not reported
- gcorso/DiffDock: README.md · Original source · 85c49b60d3e0b0182a59ee43a34a6d7036981284
- diffdockl: Primary paper PDF · Original source · 2402.18396v1
- gcorso/DiffDock: LICENSE · Original source · 85c49b60d3e0b0182a59ee43a34a6d7036981284
Technical metadata and extraction receipts
Stable ID: catalog-model-diffdock-l
- areas
- molecular-interactions
- method types
- specialist
- entity level
- family
- version
- 2024 release
- reported name
- DiffDock-L
- access
- Public pose-prediction code and weights; no native affinity prediction.
- method type
- specialist
- historical missing metadata
- checkpoint revision: not_yet_extracted; training data: not_yet_extracted; licence: not_yet_extracted
- 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.
- entity classification
- review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-official-fa7a6c37148223466dee; evidence-official-fffd4026cb8f4018fe2e; source locator: DiffDock-L paper Section 5.1 and Figure 3; official README: February 2024 update and License; ambiguities: None recorded
Related records
- family: DiffDock-L