  The emerging field of hybrid DNA - protein nanotechnology brings with it the
potential for many novel materials which combine the addressability of DNA
nanotechnology with versatility of protein interactions. However, the design
and computational study of these hybrid structures is difficult due to the
system sizes involved. To aid in the design and in silico analysis process, we
introduce here a coarse-grained DNA/RNA-protein model that extends the
oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on
an anisotropic network model representation. Fully equipped with analysis
scripts and visualization, our model aims to facilitate hybrid nanomaterial
design towards eventual experimental realization, as well as enabling study of
biological complexes. We further demonstrate its usage by simulating
DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in
polymerase.
