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 passages

2 evaluations · 2 results

Overview

Datasets

BioDolphin 1.1-derived lipid–protein complexes curated against PDB structural information.

Metrics

Top-ranked lipid RMSD is compared with each method’s confidence or affinity score.

Allowed inputs

Lipid and protein inputs for pose prediction.

Sources

Evaluation procedure diagram

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

2 evaluations · 2 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Chai-1	Task: Lipid–protein binding pose Dataset: LiPP lipid–protein complexes	60.7 Success rate, ligand all-atom RMSD <2 Å % · unknown Uncertainty: 95% CI 55.2–66.0 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Chai-1: 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, Chai-1 row, LiPP (N=331) % Success Rate column
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 checked Methods, coverage and source DiffDock-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 2026-09-29-06401fd5b220.

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation 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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Run instructions

No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-ff2dec63c5a3dd

Specifications

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.

Data, procedure and scoring
Property	Description and evidence
Datasets	BioDolphin 1.1-derived lipid–protein complexes curated against PDB structural information. 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
Splits	Post-cutoff structures form a test subset; older structures remain in a separately labelled precutoff subset. 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
Metrics	Top-ranked lipid RMSD is compared with each method’s confidence or affinity score. 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
Baselines	AlphaFold3, Chai-1, RoseTTAFold All-Atom, DiffDock-L and AutoDock Vina. 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
Leakage controls	The temporal cutoff is selected after the most recent stated training/calibration cutoff among compared tools. 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
Uncertainty	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 passages
Entity type	Paper-specific computational evaluation 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 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 sources Sources The 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. 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
Allowed inputs	Lipid and protein inputs for pose prediction. 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
Adaptation	Pretrained structure/docking methods are tested on pre-cutoff and post-cutoff structures separately. 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

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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

Historical gaps recorded on 2026-09-17

The catalogue now holds 2 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.

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

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.

17 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.548973+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: needs review

2 source records and release history

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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

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