Computational protocol: Stereochemistry and amyloid inhibition: Asymmetric triplex metallohelices enantioselectively bind to Aβ peptide

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Protocol publication

[…] We obtained the structure of the Aβ40 from the PDB (NMR structure in aqueous solution, PDB 2LFM). Specifically, the structures of Aβ40 and the metallohelices (ΛA1, ΔA1, ΛB4, and ΔB4) were prepared by using AutoDock Tools. The torsion angles of these metallohelices were regarded as flexible. Binding calculations were carried out between Aβ40 and the metallohelices by AutoDock Vina. In the docking study, the exhaustiveness for the docking runs was 400. The starting positions of the metallohelices were randomly determined, and 20 modes of docking were obtained during docking. Docked models of the metallohelices with Aβ40 were visualized using Discovery Studio. […]

Pipeline specifications

Software tools AutoDock, AutoDock Vina
Application Protein interaction analysis
Organisms Caenorhabditis elegans
Diseases Alzheimer Disease, Drug-Related Side Effects and Adverse Reactions