PoseBusters version 2, 308 protein-small molecule complexes; success rates taken from the literature by the LiPP authors.
4 evaluations · 4 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AutoDock Vina (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, PoseBusters v2 Dataset: PoseBusters v2 (308 protein-small molecule complexes) | 58% Success rate (RMSD below 2 Angstrom and PoseBusters valid; PoseBusters v2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceAutoDock Vina on PoseBusters v2 (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-posebusters-v2-308 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 3, row 'AutoDock Vina', column 'PoseBusters v2 (N = 308) % Success Rate' |
| Configuration: AlphaFold 3 (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v2 Dataset: PoseBusters v2 (308 protein-small molecule complexes) | †80.5 {75.6–84.8}% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2) percent · higher Uncertainty: 95% CI 75.6 to 84.8. Exact binomial interval (table footnote a: 'lower and upper bounds of the 95% confidence intervals calculated with exact binomial distribution') Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceAlphaFold 3 on PoseBusters v2 (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-posebusters-v2-308 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, row 'AlphaFold 3', column 'PoseBusters v2 (N = 308) % Success Rate' |
| 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) | 60% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceAutoDock Vina on PoseBusters v2 (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-posebusters-v2-308 Aggregation: Not reported 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' |
| Configuration: DiffDock-L (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v2 Dataset: PoseBusters v2 (308 protein-small molecule complexes) | 50% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDiffDock-L on PoseBusters v2 (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-posebusters-v2-308 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, row 'DiffDock-L', column 'PoseBusters v2 (N = 308) % Success Rate' |
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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population 308 complexes (PoseBusters v2) Context-only references | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Version: PMC13292216.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Source location Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Context-only references | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Version: PMC13292216.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Split PoseBusters v2 Context-only references | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Version: PMC13292216.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Total 308 Context-only references | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Version: PMC13292216.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Description PoseBusters version 2, 308 protein-small molecule complexes; success rates taken from the literature by the LiPP authors. Context-only references | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Version: PMC13292216.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Name PoseBusters v2 (308 protein-small molecule complexes) Context-only references | The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods Tables 2 and 3 column headings; Table 3 footnote a ('N denotes the total number of complexes in each dataset') Version: PMC13292216.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: lit-structure-20261011-lipp-data-posebusters-v2-308