Result

Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set) of AutoDock Vina (LiPP evaluation) on LiPP benchmark set (331 lipid-protein complexes)

47.7 {42.2–53.2}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set)

Methods

Tested configuration: AutoDock Vina (LiPP evaluation)
Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, Full LiPP set
Dataset: LiPP benchmark set (331 lipid-protein complexes)
Procedure: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, Full LiPP set
Evaluation: AutoDock Vina on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom)
Coverage: Not reported scored / Not reported eligible
Uncertainty: 95% CI 42.2 to 53.2. Exact binomial interval (table footnote a: 'lower and upper bounds of the 95% confidence intervals calculated with exact binomial distribution')
Evidence: Independent external evaluation · source checkedThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, row 'AutoDock Vina', column 'LiPP (N = 331) % Success Rate'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Full LiPP set
Adaptation: None; tools run as released
Scoring implementation: lipid pose all-atom RMSD below 2 Angstrom

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Reported result 47.7 {42.2–53.2} Individual claims	The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Original source ↗ Table 2, row 'AutoDock Vina', column 'LiPP (N = 331) % Success Rate' Version: PMC13292216.1 Retrieved: 2026-09-17T07:56:27.507412+00:00	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 independent paper Audit details Extraction: Parsed the pinned Europe PMC JATS XML with extract_lipp.py (table-wrap grid with rowspan and colspan expanded); row and column labels asserted. Table 2, row 'AutoDock Vina', column 'LiPP (N = 331) % Success Rate' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md. Field: `attributes.printed_value` Source artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact Extraction artifact SHA-256: `6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e` Extraction artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Original source · PMC13292216.1

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Technical metadata and extraction receipts

Stable ID: lit-structure-20261011-lipp-result-rmsd-lipp-331-autodock-vina

metric: ligand-rmsd-under-2a-rate
metric direction: higher
unit: percent
printed value: 47.7 {42.2–53.2}
source locator: Table 2, row 'AutoDock Vina', column 'LiPP (N = 331) % Success Rate'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Reviewer re-retrieved the Europe PMC JATS XML and matched its SHA-256; an independent table-grid parse matched all 27 results and all 22 confidence intervals; a hand sample of all 27 values against the rendered PMC HTML matched.; reviewer: claude; reviewer note: Claude review agent reviewer-ps-2, independent of the extractor lit-protein-structure; no human review claimed; date: 2026-10-11; artifact sha256: 6ff34f2f709a14858a3753abf9f8f6efa1e7e3c351f15c70cf64264193a9414e; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13292216/fullTextXML; note: Extraction: Parsed the pinned Europe PMC JATS XML with extract_lipp.py (table-wrap grid with rowspan and colspan expanded); row and column labels asserted. Table 2, row 'AutoDock Vina', column 'LiPP (N = 331) % Success Rate' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md.
numeric value: 47.7
metric qualifier: lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set
uncertainty: type: confidence_interval; printed: 47.7 {42.2–53.2}; lower: 42.2; upper: 53.2; level: 0.95; method: analytic; note: Exact binomial interval (table footnote a: 'lower and upper bounds of the 95% confidence intervals calculated with exact binomial distribution')
printed value basis: Percentage as printed, with the 95% confidence interval in braces

Related records

evaluation: AutoDock Vina on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom)

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