Sentence examples for a reference ensemble of from inspiring English sources

We thus generated a reference ensemble of the GB1 domain using an MD simulation with the CHARMM22 topology format and force-field [42] with a modified backbone potential [43] and a generalized Born solvent model [44].

We validated this approach by analyzing the distribution of gene counts per COG category as a function of the score threshold (Fig. 1B; Supplementary Fig. S3) and comparing it with a reference ensemble of 18 known SOS regulons (Supplementary Table S2).

Using synthetic data we find that an ensemble that has been determined by ensemble-refinement is more similar to a reference ensemble than an ensemble determined using standard single-molecule refinement.

Using the local mean of the received power as a reference, the ensemble of fade depths for a specific location was calculated as [16].

Finally, the projection of the reference ensemble revealed that the distribution of conformations is bimodal because of a small structural change that occurred during the MD simulation.

This plot clearly shows that at all dimensions the ensemble determined using <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0004203.e130.PNG" class= inline-graphic"/> is more similar to the reference ensemble than any of the other four ensembles.

In this ensemble, the exact times of all calls are randomly reshuffled, so that the links of the reference ensemble networks have the same number of calls as the original networks, but their timings are now uncorrelated, with the exception of the daily/weekly call frequency pattern at the network level.

The first of the plots show the density of the reference ensemble, and its bimodal character is evident.

However, these approaches are only indirect methods for quantifying to what extent one can recover the correct distribution of conformations, and do not take full advantage of the fact that all structural details of the reference ensemble are known.

Together, these observations suggest that, in the case studied here, the <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0004203.e148.PNG" class= inline-graphic"/> is not only too 'precise' (ensemble is too narrow), but may also be somewhat 'inaccurate' (centre of distribution does not coincide with that of the reference ensemble).

The studies described here have not been aimed at examining this question, and may be biased by the bi-modal nature of the reference ensemble used to generate the restraints.