Some programs that might be useful to,

• Extract thermodynamics information from UV-monitored melting curves for triplex nucleic acids: here
• Caculate the sugar pucker for RNA/DNA nucleotides: here
• Back-calculate residual dipolar couplings from MD trajectories: here
• Calculate interaction energies between groups of protein/DNA atoms: here
• Extract the fraction of native base-pairs from and MD trajectory of nucleic acids: here