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