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. Author manuscript; available in PMC: 2016 Apr 14.
Published in final edited form as: J Chem Theory Comput. 2015 Mar 11;11(4):1792–1808. doi: 10.1021/ct5009558

Figure 1.

Figure 1

Illustration of the coarse-grained models of polypeptide and nucleotide chains, UNRES and NARES-2P, respectively. In UNRES, the interacting sites are peptide groups (shaded spheres labeled p) and side chains (shaded ellipsoids labeled SC). The white spheres represent α carbon atoms (labeled Cα), which are introduced to define the geometry of the backbone. In NARES-2P, the interacting sites are phosphate groups (blue spheres labeled P) and nucleic-acid bases (blue ellipsoids labeled B). A white sphere represents the sugar ring (labeled S); P and S are used to define the geometry of the backbone. The components of the protein-nucleic acid mean-field interaction in the UNRES+NARES-2P representation are also shown as red dashed lines.