Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
Lipid–protein binding pose
Lipid–protein pose prediction evaluates curated experimental structures while distinguishing pre- and post-training-cutoff examples.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passagesAt a glance
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 | BioDolphin 1.1-derived lipid–protein complexes curated against PDB structural information.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Splits | Post-cutoff structures form a test subset; older structures remain in a separately labelled precutoff subset.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Metrics | Top-ranked lipid RMSD is compared with each method’s confidence or affinity score.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Baselines | AlphaFold3, Chai-1, RoseTTAFold All-Atom, DiffDock-L and AutoDock Vina.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Leakage controls | The temporal cutoff is selected after the most recent stated training/calibration cutoff among compared tools.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Uncertainty | Success-rate intervals are computed with the exact binomial distribution.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Entity type | Paper-specific computational evaluation protocol.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Organisms | LiPP selects BioDolphin/PDB lipid–protein structures by quality, ligand class and redundancy. Dataset curation and coverage analyses describe protein functions/families and lipid classes but do not tabulate organism composition. · Not reported in inspected sourcesSourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Materials and Methods: LiPP curation; Results: dataset coverage |
| Assays | BioDolphin/PDB structural references.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Allowed inputs | Lipid and protein inputs for pose prediction.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
| Adaptation | Pretrained structure/docking methods are tested on pre-cutoff and post-cutoff structures separately.SourcesThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passagesEvaluation methodology
BioDolphin 1.1-derived lipid–protein complexes curated against PDB structural information. Post-cutoff structures form a test subset; older structures remain in a separately labelled precutoff subset. Top-ranked lipid RMSD is compared with each method’s confidence or affinity score. AlphaFold3, Chai-1, RoseTTAFold All-Atom, DiffDock-L and AutoDock Vina. The temporal cutoff is selected after the most recent stated training/calibration cutoff among compared tools. Success-rate intervals are computed with the exact binomial distribution.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passagesRecorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Chai-1: Lipid–protein binding pose Top-scoring pose; all-atom lipid RMSD below 2 Å. Independent external evaluation · Evaluation metadata: needs review | ||
| 60.7 Success rate, ligand all-atom RMSD <2 Å Unit: % · Direction: unknown | Uncertainty: 95% CI 55.2–66.0 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, Chai-1 row, LiPP (N=331) % Success Rate column Source checking is not independent reproduction. |
| 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. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods | PMC13292216.1 | Read source DOI: 10.1021/acs.jcim.6c01457 |
What is still missing
- Complete raw tables acquired. RMSD-only versusRMSD+physicalvalidity separate;95%exactbinomialCI onLiPP, prior PoseBusters numbers quoted and notnewindependent runs. Structured extraction pending.
Search and extraction details
source found structured extraction pending
Searches
- The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods primary paper benchmark results
Evidence locations
- Tables2–3;LiPP331/LiPPtest36/PoseBusters cohorts and sampling
Strengths and limitations
Limitations and conditions
- Temporal exclusion does not establish complete sequence/ligand dissimilarity. Scores from different tools have different meanings and are not interchangeable uncertainty estimates.
Sources
The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; 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-ff2dec63c5a3ddEvidence 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.
17 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 | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 ["Input: Lipid and protein inputs for pose prediction.","Evaluation: Pretrained structure/docking methods are tested on pre-cutoff and post-cutoff structures separately.","Readout: Top-ranked lipid RMSD is compared with each method’s confidence or affinity score."] Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 BioDolphin 1.1-derived lipid–protein complexes curated against PDB structural information. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 Post-cutoff structures form a test subset; older structures remain in a separately labelled precutoff subset. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 Pretrained structure/docking methods are tested on pre-cutoff and post-cutoff structures separately. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 Top-ranked lipid RMSD is compared with each method’s confidence or affinity score. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 AlphaFold3, Chai-1, RoseTTAFold All-Atom, DiffDock-L and AutoDock Vina. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 The temporal cutoff is selected after the most recent stated training/calibration cutoff among compared tools. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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 |
| Uncertainty Success-rate intervals are computed with the exact binomial distribution. Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; uncertainty/repeat-run/statistical-comparison passages Version: PMC13292216.1 | 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
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 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
- The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Original source · PMC13292216.1
Technical metadata and extraction receipts
Stable ID: reported-task-ff2dec63c5a3dd
- areas
- molecular-interactions
- tasks
- Lipid–protein binding pose
- entity level
- task
- version
- Not reported
- task
- Lipid–protein binding pose
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-lipp-2026-6ff34f2f709a; inspected locators: Tables2–3;LiPP331/LiPPtest36/PoseBusters cohorts and sampling; searched queries: The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods primary paper benchmark results; gaps: Complete raw tables acquired. RMSD-only versusRMSD+physicalvalidity separate;95%exactbinomialCI onLiPP, prior PoseBusters numbers quoted and notnewindependent runs. Structured extraction pending.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- 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: lipp-2026; source locator: Methods: Curation of LiPP; test/precutoff separation; Evaluation of Scoring Power; cached text lines 12–16, 50–51; 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.
Related records
- dataset: LiPP lipid–protein complexes
- benchmark: Chai-1: Lipid–protein binding pose
- benchmark: DiffDock-L: Lipid–protein binding pose