Molecular docking of sphingomyelin along the hydrophobic groove of hSMPD2

JY Jingbo Yi
BQ Boya Qi
JY Jian Yin
RL Ruochong Li
XC Xudong Chen
JH Junhan Hu
GL Guohui Li
SZ Sensen Zhang
YZ Yuebin Zhang
MY Maojun Yang
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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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