The initial conformation of sphingomyelin was manually placed along the hydrophobic groove of hSMPD2 and the RosettaLigand docking protocol51 was used for molecular docking with a library of 300 conformations of sphingomyelin selected from CHARMM-GUI archive for biomembrane systems52.
The script for the docking protocol is available at: https://github.com/yuebinzhang/Yi_et_at_hSMPD2_Nat_Comm/tree/main/RosettaLigand_docking/.
The conformation with a minimum distance between the magnesium ion and the non-bridging oxygen atom of the phosphate group of sphingomyelin was used for further hydrolysis mechanism investigation.
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