This piece of code uses the HelixMC package to simulate the stability of tecto-RNA.

You will need to first install python (v2.7) and following packages:

• scikit-learn (http://scikit-learn.org/stable/)
• HelixMC (https://github.com/fcchou/HelixMC)

HelixMC/scikit-learn also depends on numpy and scipy.

The main simulation code is simu_tecto.py. To get a list to brief description of avaliable options, simply run python simu_tecto.py -h.

Here is a simple command line example:

python simu_tecto.py -seq1 GGGGGGGGGGGG CCCCCCCCCCCC -n_cycles 1000

After the run you will get output that looks like:

Log likelyhood score: -11.8090588021
Free energy: 6.96734469322

Also two files helix1_bp.par and helix2_bp.par will be generated, containing the parameters for the best helical conformer for forming tecto-RNA in the simulation. These files can be then used to generate pdb files.

The pdb files can be generated using Web3DNA (http://w3dna.rutgers.edu/).

In the Web3DNA homepage, click Reconstruction on the top stripe. Then select Customized model. In the dropdown menu, choose Customized base-pair-step/nucleotide parameter, then click Continue.

Now in the Backbone conformation dropdown menu, select RNA-form. For the Base-pair parameter file, upload one of the previously generated file (e.g. helix1_bp.par). Then click Build. Downloas the generated pdb file, and repeat the process for the other helix.