AutoDock Vina (LiPP evaluation)

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Evaluations and results

6 evaluations · 6 results. Different protocols are not a single leaderboard.

Sorted by Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2) (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	Protocol and dataset	Ligand RMSD under 2a rate (ligand pose RMSD below 2 Angstrom, as reported in the cited literature; PoseBusters v2)	Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; Full LiPP set)	Ligand RMSD under 2a rate (lipid pose all-atom RMSD below 2 Angstrom; LiPP test set)	Success rate (RMSD below 2 Angstrom and PoseBusters valid; Full LiPP set)	Success rate (RMSD below 2 Angstrom and PoseBusters valid; LiPP test set)	Success rate (RMSD below 2 Angstrom and PoseBusters valid; PoseBusters v2)
AutoDock Vina (LiPP evaluation)Evaluation	LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, PoseBusters v2, PoseBusters v2 (308 protein-small molecule complexes)	60%	Not reported	Not reported	Not reported	Not reported	Not reported
AutoDock Vina (LiPP evaluation)Evaluation	LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, Full LiPP set, LiPP benchmark set (331 lipid-protein complexes)	Not reported	Not reported	Not reported	45.9 {40.4–51.4}%	Not reported	Not reported
AutoDock Vina (LiPP evaluation)Evaluation	LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, LiPP test set, LiPP test set (36 complexes released after every tool's cutoff)	Not reported	Not reported	Not reported	Not reported	30.5 {16.3–48.1}%	Not reported
AutoDock Vina (LiPP evaluation)Evaluation	LiPP Table 3: RMSD below 2 Angstrom and PoseBusters valid, PoseBusters v2, PoseBusters v2 (308 protein-small molecule complexes)	Not reported	Not reported	Not reported	Not reported	Not reported	58%
AutoDock Vina (LiPP evaluation)Evaluation	LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, Full LiPP set, LiPP benchmark set (331 lipid-protein complexes)	Not reported	47.7 {42.2–53.2}%	Not reported	Not reported	Not reported	Not reported
AutoDock Vina (LiPP evaluation)Evaluation	LiPP Table 2: lipid pose all-atom RMSD below 2 Angstrom, LiPP test set, LiPP test set (36 complexes released after every tool's cutoff)	Not reported	Not reported	30.5 {16.3–48.1}%	Not reported	Not reported	Not reported

All 6 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
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, 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 checked Methods, coverage and source AutoDock 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: 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 checked Methods, coverage and source AutoDock 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: 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 checked Methods, coverage and source AutoDock 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: 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 checked Methods, coverage and source AutoDock 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: 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: 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 checked Methods, coverage and source AutoDock 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'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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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-config-autodock-vina

areas: protein-structure; molecular-interactions
contexts: research
method types: conventional_pipeline
reported name: AutoDock Vina
method role: physics-based docking
training setting: Scoring function was weighted using PDBbind before 2019
foundation model eligible: false
source locator: Table 1, row 'AutoDock Vina'; Tables 2 and 3 row labels
missing metadata: version: reason: unreported; note: Tool versions are not printed in Tables 1 to 3
provenance note: AutoDock Vina as run on the LiPP benchmark set by the LiPP authors.

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