Computational protocol: A single amino acid determines the toxicity of Ginkgo biloba extracts

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Protocol publication

[…] RDL was aligned with GLIC using FUGUE (), and the RDL receptor pore homology model was generated using Modeller 9.8 (), based on the crystal structure of GLIC [Protein Data Bank (PDB) ID: 3EAM]. The best model was selected after Ramachandran plot analysis of all the generated models. Docking of compounds into the homology model was performed using GOLD 3.0 (Cambridge Crystallographic Data Centre, Cambridge, UK). The binding site was defined as a 15-Å-radius docking sphere surrounding the Cα of the 6′ residues in chains A and C. Ten genetic algorithm runs were performed on each docking exercise using default parameters. The structures were visualized and hydrogen bonds were identified using PyMOL 1.3 (DeLano Scientific LLC, South San Francisco, CA, USA). […]

Pipeline specifications

Software tools FUGUE, MODELLER, PyMOL
Application Protein structure analysis
Organisms Ginkgo biloba, Homo sapiens
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals gamma-Aminobutyric Acid, Ginkgolides