The 36 LiPP complexes released after the training or calibration cutoff of every tool evaluated.
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, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 25.0 {12.1–42.2}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; LiPP test set) percent · higher Uncertainty: 95% CI 12.1 to 42.2. 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 sourceAlphaFold 3 on LiPP test set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: AutoDock Vina (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 30.5 {16.3–48.1}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; LiPP test set) percent · higher Uncertainty: 95% CI 16.3 to 48.1. 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 sourceAutoDock Vina on LiPP test set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: Chai-1 (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 16.6 {6.3–32.8}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; LiPP test set) percent · higher Uncertainty: 95% CI 6.3 to 32.8. 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 | Independent external evaluation · Source checkedMethods, coverage and sourceChai-1 on LiPP test set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: DiffDock-L (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 8.3 {1.7–22.4}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; LiPP test set) percent · higher Uncertainty: 95% CI 1.7 to 22.4. 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 sourceDiffDock-L on LiPP test set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: RoseTTAFold AA (LiPP evaluation) | Protocol: LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 2.7 {0.07–14.5}% Success rate (RMSD below 2 Angstrom and PoseBusters valid; LiPP test set) percent · higher Uncertainty: 95% CI 0.07 to 14.5. 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 sourceRoseTTAFold AA on LiPP test set (RMSD below 2 Angstrom and PoseBusters valid) lit-structure-20261011-lipp-protocol-pb-valid-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: AlphaFold 3 (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 47.2 {30.4–64.5}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set) percent · higher Uncertainty: 95% CI 30.4 to 64.5. 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 LiPP test set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: AutoDock Vina (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 30.5 {16.3–48.1}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set) percent · higher Uncertainty: 95% CI 16.3 to 48.1. 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 sourceAutoDock Vina on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: Chai-1 (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 36.1 {20.8–53.7}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set) percent · higher Uncertainty: 95% CI 20.8 to 53.7. 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 sourceChai-1 on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: DiffDock-L (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 30.5 {16.3–48.1}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set) percent · higher Uncertainty: 95% CI 16.3 to 48.1. 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 LiPP test set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-test-36 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 test set (N = 36) % Success Rate' |
| Configuration: RoseTTAFold AA (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set Dataset: LiPP test set (36 complexes released after every tool's cutoff) | 11.1 {3.1–26.0}% Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set) percent · higher Uncertainty: 95% CI 3.1 to 26.0. 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 sourceRoseTTAFold AA on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-lipp-test-36 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 test set (N = 36) % Success Rate' |
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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population 36 complexes (LiPP test 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 LiPP test 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 36 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 36 LiPP complexes released after the training or calibration cutoff of every tool evaluated. 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 test set (36 complexes released after every tool's cutoff) 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-test-36