Sentence examples for templates the predicted from inspiring English sources

As expected using these templates, the predicted shape for the HbpR A-domain was highly similar to those of XylR and DmpR with exception of a few loops (Fig. 1D, E).

In 2009, Oh et al. [24] developed LEE, a two-stage template-based ligand binding site prediction method, where templates are used first for protein 3D modeling and then for binding site prediction by structural clustering of ligand-containing templates to the predicted 3D model.

PCR amplification using the 2HA and R108 templates yielded the predicted junction fragments, confirming the genome structures shown in Fig.  1 and Supplementary Fig. S1 (primer pairs 12.909F-13.689R and S7_57758F-58.549R, and 13.689R-58647R and 12.821F-58.118F, respectinely, in Supplementary Table S1).

We confirmed the presence of this duplication using real time PCR to quantify genomic DNA template near the predicted ends of the duplication (Table S2) and subsequently used PCR with primers directed across the predicted duplication; such primers would only produce a product in the presence of a tandem duplication (reverse primers P3 or P4 and forward P11, see Figure 1 and Table S2).

The ribbon diagram of the template and the predicted structure of LdRuvB1 and LdRuvB2 were superimposed.

To obtain the structural characteristics of the trihelix family, the sequences from each clade were aligned by the Align 2D structure alignment program using Arabidopsis GT1 as a template and the predicted structures were evaluated.

Functionally, the choice of templates will bias the predicted model.

One approach is to model the putative homologs using the resolved crystallographic or NMR 3D protein structures of the most closely related organisms as templates and determine the predicted thermodynamic stability and probability of the putative structures using computer algorithms.

The LUT information for each template should contain two parts, the template index and the predicted gray value,.

The table lists the ORFan name, the 3D-Jury score, the PDB template used and the predicted SCOP fold type.

Figure 5(c) shows the alignment between the final model and the chosen template, indicating that the predicted tertiary structure was preserved during the MD simulation.