Model type
Molecular docking model; this record is the paper-specific evaluated configuration.
Configuration
DiffDock-L
This configuration predicts lipid–protein poses in the LiPP benchmark.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Results/Curation of the LiPP Benchmark Set for Modeling Lipid–Protein Interactions (paragraph 1); Materials and Methods/Curation of the LiPP Test Set, Precutoff Set, and Similarity Assessments between the Different LiPP Data Sets (paragraph 2)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
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2)At a glance
Biological inputs
Experimental protein and lipid coordinates, without a predefined binding pocket
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Materials and Methods/DiffDock-L (paragraph 1)Outputs
Lipid–protein complex or docking-pose coordinates
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Protein Structure Errors (paragraph 1); Materials and Methods/Molecular Docking and Structure Prediction Protocols (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-L: Lipid–protein binding pose Top-scoring pose; all-atom lipid RMSD below 2 Å. Independent external evaluation · Evaluation metadata: needs review | ||
| 46.8 Success rate, ligand all-atom RMSD <2 Å Unit: % · Direction: unknown | Uncertainty: 95% CI 41.3–52.3 Scored: Not reported · Eligible: Not reported | source checkedThe 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. |
How it works
How the evaluated method works
DiffDock-L performs blind docking; the benchmark retains the highest-ranked pose and applies physical-plausibility checks without additional refinement.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2)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-L: Lipid–protein binding pose. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-042Strengths and limitations
Strengths and considerations
- Tests lipid chemistry and physical plausibility alongside RMSD.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Results/Protein Prediction Errors in Structure Prediction Methods (paragraph 1); Materials and Methods/Protein Structure Errors (paragraph 1)
Limitations and conditions
- Input information differs between docking and co-folding methods, and the post-cutoff test subset is much smaller than the full benchmark.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Results/Protein Prediction Errors in Structure Prediction Methods (paragraph 1); Results/Curation of the LiPP Benchmark Set for Modeling Lipid–Protein Interactions (paragraph 3)
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-51ed86132346a0Specifications
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-L performs blind docking; the benchmark retains the highest-ranked pose and applies physical-plausibility checks without additional refinement.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2) |
| Biological inputs | Experimental protein and lipid coordinates, without a predefined binding pocketSourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Materials and Methods/DiffDock-L (paragraph 1) |
| Outputs | Lipid–protein complex or docking-pose coordinatesSourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods/Protein Structure Errors (paragraph 1); Materials and Methods/Molecular Docking and Structure Prediction Protocols (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)The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods; gcorso/DiffDock README.md · Materials and Methods/Curation of the LiPP Benchmark Set; Materials and Methods/Curation of the LiPP Test Set, Precutoff Set, and Similarity Assessments between the Different LiPP Data Sets; Materials and Methods/Protein Similarity; Materials and Methods/Lipid Similarity; Materials and Methods/Molecular Docking and Structure Prediction Protocols; Materials and Methods/AlphaFold 3; Materials and Methods/Chai-1; Materials and Methods/RoseTTAFold AA; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | DiffDock-L1.1.3;20 diffusion steps, tenposes, expbeta noise schedule; best confidence pose is evaluated.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods / DiffDock-L |
| Training data / fitting | Table 1 identifies PDBbind complexes before 2019 as the training set. The LiPP evaluation uses released inference defaults without additional refinement or retraining.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 1, DiffDock-L row; Materials and Methods / Molecular Docking and Structure Prediction Protocols |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods; gcorso/DiffDock README.md · Materials and Methods/Curation of the LiPP Benchmark Set; Materials and Methods/Curation of the LiPP Test Set, Precutoff Set, and Similarity Assessments between the Different LiPP Data Sets; Materials and Methods/Protein Similarity; Materials and Methods/Lipid Similarity; Materials and Methods/Molecular Docking and Structure Prediction Protocols; Materials and Methods/AlphaFold 3; Materials and Methods/Chai-1; Materials and Methods/RoseTTAFold AA; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| 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.
22 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 | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2) Version: PMC13292216.1 | 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 ["Experimental protein and lipid coordinates, without a predefined binding pocket","DiffDock-L","Lipid–protein complex or docking-pose coordinates"] Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2) Version: PMC13292216.1 | 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 | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2) Version: PMC13292216.1 | 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-L performs blind docking; the benchmark retains the highest-ranked pose and applies physical-plausibility checks without additional refinement. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2) Version: PMC13292216.1 | 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 Experimental protein and lipid coordinates, without a predefined binding pocket Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Materials and Methods/DiffDock-L (paragraph 1) Version: PMC13292216.1 | 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 Lipid–protein complex or docking-pose coordinates Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Protein Structure Errors (paragraph 1); Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1) Version: PMC13292216.1 | 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 | gcorso/DiffDock README.md Materials and Methods/Curation of the LiPP Benchmark Set; Materials and Methods/Curation of the LiPP Test Set, Precutoff Set, and Similarity Assessments between the Different LiPP Data Sets; Materials and Methods/Protein Similarity; Materials and Methods/Lipid Similarity; Materials and Methods/Molecular Docking and Structure Prediction Protocols; Materials and Methods/AlphaFold 3; Materials and Methods/Chai-1; Materials and Methods/RoseTTAFold AA; 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 |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Materials and Methods/Curation of the LiPP Benchmark Set; Materials and Methods/Curation of the LiPP Test Set, Precutoff Set, and Similarity Assessments between the Different LiPP Data Sets; Materials and Methods/Protein Similarity; Materials and Methods/Lipid Similarity; Materials and Methods/Molecular Docking and Structure Prediction Protocols; Materials and Methods/AlphaFold 3; Materials and Methods/Chai-1; Materials and Methods/RoseTTAFold AA; 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: PMC13292216.1 | 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
- The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Original source · PMC13292216.1
- gcorso/DiffDock README.md · Original source · 85c49b60d3e0b0182a59ee43a34a6d7036981284
- gcorso/DiffDock LICENSE · Original source · 85c49b60d3e0b0182a59ee43a34a6d7036981284
Technical metadata and extraction receipts
Stable ID: reported-model-51ed86132346a0
- areas
- molecular-interactions
- entity level
- method
- version
- Not reported
- reported name
- DiffDock-L
- 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: lipp-2026; evidence-reported-base-diffdock-readme-md; source locator: Materials and Methods/Molecular Docking and Structure Prediction Protocols (paragraph 1); Results/Physical Plausibility of Docking and Structure Prediction Generated Models of Lipid–Protein Complex (paragraph 2) | README.md model description | Results/Curation of the LiPP Benchmark Set for Modeling Lipid–Protein Interactions (paragraph 1); Materials and Methods/Curation of the LiPP Test Set, Precutoff Set, and Similarity Assessments between the Different LiPP Data Sets (paragraph 2); 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.