Molecular Dynamics of TLR4/MD2/Glycolipid

TLR4/MD2/Glycolipid Molecular Dynamics Simulations Summary Molecular dynamics of an innate immunity receptor TLR4/MD2 with different glycolipids to disentangle the atomic/molecular characteristics that determine the agonist/antagonist activity. These molecular dynamics were employed to train a graph-neural network using specific sub-selections of the system. Initial Structures Antagonist complexes: Initial 3D geometries for the antagonist complexes (FP7 and FP12) were constructed by docking FP7 and FP12 into reported models of monomeric TLR4/MD2 in the antagonist conformation. Agonist complexes: Initial 3D geometries for the agonist complexes (FP11 and FP18) were generated by superimposing docked poses of FP11 and FP18 onto reported 3D structures of the active (TLR4/MD2)₂ dimer complex.