Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2) of AutoDock Vina (LiPP evaluation) on PoseBusters v2 (308 protein-small molecule complexes)
60% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2)
Methods
- Tested configuration
- AutoDock Vina (LiPP evaluation)
- Protocol
- LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v2
- Dataset
- PoseBusters v2 (308 protein-small molecule complexes)
- Procedure
- LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v2
- Evaluation
- AutoDock Vina on PoseBusters v2 (lipid pose all-atom RMSD below 2 Angstrom)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Result quoted from another source · source checkedThe LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, row 'AutoDock Vina', column 'PoseBusters v2 (N = 308) % 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
- PoseBusters v2
- 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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 60 Individual claims | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Table 2, row 'AutoDock Vina', column 'PoseBusters v2 (N = 308) % Success Rate' Version: PMC13292216.1 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 paper compilation Audit detailsExtraction: 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 'PoseBusters v2 (N = 308) % 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: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. Extraction artifact SHA-256: |
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
Technical metadata and extraction receipts
Stable ID: lit-structure-20261011-lipp-result-rmsd-posebusters-v2-308-autodock-vina
- metric
- ligand-rmsd-under-2a-rate
- metric direction
- higher
- unit
- percent
- printed value
- 60
- source locator
- Table 2, row 'AutoDock Vina', column 'PoseBusters v2 (N = 308) % 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 'PoseBusters v2 (N = 308) % 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
- 60
- metric qualifier
- ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2
- missing metadata
- uncertainty: reason: unreported
- printed value basis
- Percentage as printed