Many biophysical studies indicate interactions with lipid/detergent molecules are critical to the folding/stability of membrane proteins, but only limited structural data are available on these interactions. In principle, atomistic molecular dynamics (MD) simulations may be used to follow the self-assembly of proteins with lipid/detergent. However, MD studies are limited to system sizes of up to ~100,000 atoms and time lengths of up to ~100 ns. Coarse grained (CG) models, in which small groups of atoms are treated collectively as large particles, provide a method for increasing timescales and system dimensions.
MemProtMD, MemProtMD, membrane protein, simulation, coarse-grained, intrinsic membrane, martini, CG