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.
Last update: 2017-10-24, 00:30