  Modeling of DNA-protein interactions is a complex process involving many
important time and length scales. This can be facilitated through the use of
coarse-grained models which reduce the number of degrees of freedom and allow
efficient exploration of binding configurations. It is known that the local
structure of DNA can significantly affect its protein-binding properties (i.e.
intrinsic curvature in DNA-histone complexes). In a step towards comprehensive
DNA-protein modeling, we expand the 3SPN.2 coarse-grained model to include
intrinsic shape, and validate the refined model against experimental data
including melting temperature, local flexibility, persistence length, and minor
groove width profile.
