Protocol

LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set

Success is a predicted lipid pose whose all-atom RMSD to the experimental pose is less than 2 Angstrom. Evaluated on LiPP test set.

5 evaluations · 5 results

Overview

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5 recorded evaluations, 5 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

5 evaluations · 5 results. Different protocols are not a single leaderboard.

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)

Sorted by Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set) (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 (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set)
AlphaFold 3 (LiPP evaluation)Evaluation	47.2 {30.4–64.5}% (best in column)
Chai-1 (LiPP evaluation)Evaluation	36.1 {20.8–53.7}%
AutoDock Vina (LiPP evaluation)Evaluation	30.5 {16.3–48.1}%
DiffDock-L (LiPP evaluation)Evaluation	30.5 {16.3–48.1}%
RoseTTAFold AA (LiPP evaluation)Evaluation	11.1 {3.1–26.0}%

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Exact evaluated configurations and original reported results
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, 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 checked Methods, coverage and source AlphaFold 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 checked Methods, coverage and source AutoDock 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 checked Methods, coverage and source Chai-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 checked Methods, coverage and source DiffDock-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 checked Methods, coverage and source RoseTTAFold 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'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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External evaluations: 5

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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

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Technical metadata and extraction receipts

Stable ID: lit-structure-20261011-lipp-protocol-rmsd-lipp-test-36

areas: protein-structure; molecular-interactions
contexts: research
protocol: Success is a predicted lipid pose whose all-atom RMSD to the experimental pose is less than 2 Angstrom. One pose per complex as the tool ranks it; the paper gives no re-ranking step.
metric: ligand-rmsd-under-2a-rate
metric direction: higher
unit: percent
success threshold: criterion: Success is a predicted lipid pose whose all-atom RMSD to the experimental pose is less than 2 Angstrom.
version: LiPP as published 2026
source locator: Table 2, column 'LiPP test set (N = 36) % Success Rate'
limitations: Per-complex identifiers are in the supplementary data and were not extracted.

Related records

part of: LiPP benchmark set
uses data: LiPP test set (36 complexes released after every tool's cutoff)
assessment: AlphaFold 3 on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom)
assessment: AutoDock Vina on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom)
assessment: Chai-1 on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom)
assessment: DiffDock-L on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom)
assessment: RoseTTAFold AA on LiPP test set (lipid pose all-atom RMSD below 2 Angstrom)
assessed by: Choose structural hypotheses to guide experiments

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