The full LiPP set of 331 experimental lipid-protein complexes curated from BioDolphin v1.1.
10 evaluations · 10 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaFold 3 (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, Full LiPP set Dataset: LiPP benchmark set (331 lipid-protein complexes) | 64.3 {58.9–69.5}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; Full LiPP set) percent · higher Uncertainty: 95% CI 58.9 to 69.5. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold 3 on Full LiPP set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-331 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 3, row 'AlphaFold 3', column 'LiPP (N = 331) % Success Rate' |
| Configuration: AutoDock Vina (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, Full LiPP set Dataset: LiPP benchmark set (331 lipid-protein complexes) | 45.9 {40.4–51.4}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; Full LiPP set) percent · higher Uncertainty: 95% CI 40.4 to 51.4. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAutoDock Vina on Full LiPP set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-331 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 'LiPP (N = 331) % Success Rate' |
| Configuration: Chai-1 (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, Full LiPP set Dataset: LiPP benchmark set (331 lipid-protein complexes) | 39.5 {34.2–45.0}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; Full LiPP set) percent · higher Uncertainty: 95% CI 34.2 to 45.0. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 on Full LiPP set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-331 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 3, row 'Chai-1', column 'LiPP (N = 331) % Success Rate' |
| Configuration: DiffDock-L (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, Full LiPP set Dataset: LiPP benchmark set (331 lipid-protein complexes) | 24.1 {19.6–29.1}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; Full LiPP set) percent · higher Uncertainty: 95% CI 19.6 to 29.1. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceDiffDock-L on Full LiPP set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-331 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 3, row 'DiffDock-L', column 'LiPP (N = 331) % Success Rate' |
| Configuration: RoseTTAFold AA (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, Full LiPP set Dataset: LiPP benchmark set (331 lipid-protein complexes) | 15.4 {11.6–19.7}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; Full LiPP set) percent · higher Uncertainty: 95% CI 11.6 to 19.7. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceRoseTTAFold AA on Full LiPP set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-331 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 3, row 'RoseTTAFold AA', column 'LiPP (N = 331) % Success Rate' |
| Configuration: AlphaFold 3 (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) | 76.1 {71.1–80.6}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set) percent · higher Uncertainty: 95% CI 71.1 to 80.6. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaFold 3 on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-331 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 'LiPP (N = 331) % Success Rate' |
| 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) | 47.7 {42.2–53.2}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set) percent · higher 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') Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAutoDock Vina on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-331 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 'LiPP (N = 331) % Success Rate' |
| Configuration: Chai-1 (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) | 60.7 {55.2–66.0}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set) percent · higher Uncertainty: 95% CI 55.2 to 66.0. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-331 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, row 'Chai-1', column 'LiPP (N = 331) % Success Rate' |
| Configuration: DiffDock-L (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) | 46.8 {41.3–52.3}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set) percent · higher Uncertainty: 95% CI 41.3 to 52.3. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceDiffDock-L on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-331 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 'LiPP (N = 331) % Success Rate' |
| Configuration: RoseTTAFold AA (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) | 37.1 {31.9–42.6}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set) percent · higher Uncertainty: 95% CI 31.9 to 42.6. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceRoseTTAFold AA on Full LiPP set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-331 Aggregation: Not reported The LiPP Benchmark Set for Modeling Lipid–Protein Complexes: Comparison of Co-Folding and Docking Methods · Table 2, row 'RoseTTAFold AA', column 'LiPP (N = 331) % Success Rate' |
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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population 331 complexes (Full LiPP set) 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 footnote a ('N denotes the total number of lipid-protein 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 footnote a ('N denotes the total number of lipid-protein 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 footnote a ('N denotes the total number of lipid-protein 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 Full LiPP set 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 footnote a ('N denotes the total number of lipid-protein 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 331 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 footnote a ('N denotes the total number of lipid-protein 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 The full LiPP set of 331 experimental lipid-protein complexes curated from BioDolphin v1.1. 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 footnote a ('N denotes the total number of lipid-protein 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 LiPP benchmark set (331 lipid-protein 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 footnote a ('N denotes the total number of lipid-protein 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-lipp-331