Computational protocol: Bile acids potentiate proton‐activated currents in Xenopus laevis oocytes expressing human acid‐sensing ion channel (ASIC1a)

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Protocol publication

[…] Putative t‐DCA binding sites in the transmembrane region of ASIC1 were predicted using molecular docking software AutoDock Vina (Trott and Olson ). The structure of the chicken ASIC1 in its open conformation (PDB: 4NTX; [Baconguis et al. ]) was modified by including the polar hydrogen atoms. The grid box defining the docking boundaries was assigned using AutoDockTools 1.5.6 (Sanner ; Morris et al. ). Structure of t‐DCA was extracted from ZINC version 12 database (ZINC ID: ZINC04282168; [Irwin and Shoichet ]). The calculation of the total energy of interaction (MolDock Score [Thomsen and Christensen ] between ASIC1 and t‐DCA was made using Molegro Molecular Viewer 2.5. […]

Pipeline specifications

Software tools AutoDock Vina, AutoDock
Application Protein interaction analysis
Organisms Xenopus laevis, Homo sapiens
Chemicals Amino Acids, Bile Acids and Salts, Sodium