David Case
 Charles Brooks
 Stephen Harvey
 Robert Tan

NAB (Nucleic Acid Builder) generates nucleic acid structures from base geometries or distance constraints.

 
Yammp allows modeling and refinement of low-resolution nucleic acid models

Yammp home page
  Documentation, Download
 
YUP (Yammp Under Python) allows modeling and refinement of low-resolution nucleic acid models through a python programming interface.
YUP is not yet released to the public, keep checking back.

YUP home page
  Documentation