LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v1
Success is a predicted small-molecule ligand pose with RMSD below 2 Angstrom to the experimental pose, as reported in the publication the LiPP authors cite. Pose selection and the RMSD atom set follow that publication and are not stated in this source. Evaluated on PoseBusters v1.
Overview
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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
3 evaluations · 3 results. Different protocols are not a single leaderboard.
Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v1 · Dataset: PoseBusters v1 (428 protein-small molecule complexes)
Sorted by Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v1) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v1) |
|---|---|
| Chai-1 (LiPP evaluation)Evaluation | 77% (best in column) |
| AlphaFold 3 (LiPP evaluation)Evaluation | †76.4 {72.1–80.3}% |
| RoseTTAFold AA (LiPP evaluation)Evaluation | 42% |
All 3 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaFold 3 (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v1 Dataset: PoseBusters v1 (428 protein-small molecule complexes) | †76.4 {72.1–80.3}% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v1) percent · higher Uncertainty: 95% CI 72.1 to 80.3. 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 | Result quoted from another source · Source checkedMethods, coverage and sourceAlphaFold 3 on PoseBusters v1 (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-posebusters-v1-428 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 v1 (N = 428) % Success Rate' |
| Configuration: Chai-1 (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v1 Dataset: PoseBusters v1 (428 protein-small molecule complexes) | 77% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceChai-1 on PoseBusters v1 (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-posebusters-v1-428 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 'PoseBusters v1 (N = 428) % Success Rate' |
| Configuration: RoseTTAFold AA (LiPP evaluation) | Protocol: LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v1 Dataset: PoseBusters v1 (428 protein-small molecule complexes) | 42% Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceRoseTTAFold AA on PoseBusters v1 (lipid pose all-atom RMSD below 2 Angstrom) lit-structure-20261011-lipp-protocol-rmsd-posebusters-v1-428 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 'PoseBusters v1 (N = 428) % Success Rate' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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Baseline coverage
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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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-protocol-rmsd-posebusters-v1-428
- areas
- protein-structure; molecular-interactions
- contexts
- research
- protocol
- Success is a predicted small-molecule ligand pose with RMSD below 2 Angstrom to the experimental pose, as reported in the publication the LiPP authors cite. Pose selection and the RMSD atom set follow that publication and are not stated in this source.
- metric
- ligand-rmsd-under-2a-rate
- metric direction
- higher
- unit
- percent
- success threshold
- criterion: Success is a predicted small-molecule ligand pose with RMSD below 2 Angstrom to the experimental pose, as reported in the publication the LiPP authors cite. Pose selection and the RMSD atom set follow that publication and are not stated in this source.
- version
- LiPP as published 2026
- source locator
- Table 2, column 'PoseBusters v1 (N = 428) % Success Rate'
- limitations
- The PoseBusters columns are literature values compiled by the LiPP authors, not their own runs.; Per-complex identifiers are in the supplementary data and were not extracted.
Related records
- part of: LiPP benchmark set
- uses data: PoseBusters v1 (428 protein-small molecule complexes)
- assessment: AlphaFold 3 on PoseBusters v1 (lipid pose all-atom RMSD below 2 Angstrom)
- assessment: Chai-1 on PoseBusters v1 (lipid pose all-atom RMSD below 2 Angstrom)
- assessment: RoseTTAFold AA on PoseBusters v1 (lipid pose all-atom RMSD below 2 Angstrom)