RNA–Ligand Interaction and Riboswitch Kinetics
This is a pipeline capable of simulating the folding kinetics of an RNA molecule in the presence
of a binding ligand. Assuming ligand excess and a single structural binding motif, the kinetics
are computed by solving a coarse-grained Markov process via diagonalization of its rate matrix.
The coarse graining is based on the idea of gradient basins in the energy landscape of the RNA.
This script allows an in silico analysis, e.g. of riboswitches, that yields much more
information than simple thermodynamic calculations that cannot consider any kinetic effects.
This software is now available via Bioconda . To install it, simply run the following command:
conda install kinsimriboswitch
Last update: 2018-10-02, 17:19