For analysis of the TNFR1 crystal structure, visual molecular dynamics (VMD) was used. The crystal structure of the preligand dimer of TNFR1 ECD was downloaded from the PDB (PDB: 1NCF) (6), and the structure preparation was performed in CHARMM-GUI. The distance measurement of the TNFR1 ECD was performed in VMD.The hydrogen bonds between the residues in the ligand-binding loop were determined by VMD with a distance cutoff of <3.2 Å and an angle cutoff of <60o.

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