  In this work we describe a set of Coarse-grained (CG) tools that allow to
simulate the uptake of the nanoparticles (NPs) coated with proteins by a lipid
bilayer. We describe a CG model to calculate the adsorption energies and the
most favorable adsorption orientations of proteins onto a hydrophobic NP. The
proposed method is then used to calculate the adsorption energies of two common
proteins in human blood onto neutral and negative charged NPs. We also report
the effect of the NP radius on the adsorption energies and validate the
proposed methodology against full atomistic simulations. We also describe a
methodology in which full atomistic simulations of a lipid bilayer and various
lipid-cholesterol mixtures are used for the extraction of CG pair potentials.
We also compare and validate the predictions of simulations at molecular and CG
level. Finally, we present a CG simulation of the interaction a bare NP and of
a NP-protein complex with a lipid bilayer.
