The average structural branchpoint distances of 1000 suboptimal structures sampled from within 5% of the MFE for each mutant are given in Table 2.
Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations.
Here, we describe an alternative procedure for the characterization of mRNA structures, in which structures sampled from the Boltzmann-weighted ensemble of RNA secondary structures are clustered.
To compare the two simulations, sampled structures were clustered using the GROMOS method: after the construction of the MxM RMSD matrix (were M is the number of structures sampled).
To obtain a qualitative description of the structures sampled along both axes, we analyzed the different unfolding trajectories based on the order in which each β-strand in the structure becomes solvent exposed.
Accordingly, structures sampled from a Gaussian distribution about the base structure should be more predictive of the base structure than structures displaying true variability.
RNA-Seq data of this study were generated from fungal infection structures sampled at six time points of the infection cycle.
The intuition here is that structures sampled from a Gaussian distribution (i.e. modeled by B-factors) about the PDB structure should be more predictive of the PDB structure than structures displaying true variability.
The digital ECG system has the advantages of simple structure, sampling with high speed and precision, powerful real-time processing ability and good quality.
Ye Ding's Sfold program [ 23] was the first to introduce stochastic structure sampling.
