Running ENCoM on RNA

ENCoM was recently adapted to work on RNA molecules, using three beads per nucleotide as described in the following article: Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation.

The adaptation is included by default in NRGTEN, thus all models will assign three beads per nucleotide in the input structure. RNA-protein complexes are also supported.

In the nrgten_examples repository, the WT and G22U variant of miR-125a are provided, called mir125a_WT.pdb and mir125a_G22U.pdb respectively. The Entropic Signature (defined in the above-referenced article) for each variant can be computed as follows:

from nrgten.encom import ENCoM
import numpy as np

wt = ENCoM("mir125a_WT.pdb")
g22u = ENCoM("mir125a_G22U.pdb")

entrosig_wt = wt.compute_bfactors_boltzmann(beta=np.e**2.25)
entrosig_g22u = g22u.compute_bfactors_boltzmann(beta=np.e**2.25)

The beta value used in this example is the one which led to the best performance (see referenced article).

Note

You can safely ignore such warnings when computing Entropic Signatures: RuntimeWarning: overflow encountered in float_power.