Sentence examples for the structural template from inspiring English sources

To predict the structure for a target protein, its sequence is threaded against all the structures in the structural template database in search of a structure with a significant "fit" to the sequence.

In the threading studies, fragments of the ERev protein have been threaded against 13,391 representative structures in the structural template library, and the model structures were obtained from the top scoring members of the top five families using MODELLER [29], [30] (see Materials and Methods).

All fragments generated in this manner were threaded against the 13,391 representative structures in the structural template library and the threading score for each fragment was calculated.

Briefly, modeling of human REP-1 was based on the 2.2 Å crystal structure of rat Rep-1 protein (PDB file: 1vg0) as the structural template (Abola et al. 1987).

A structural homology model of EFL was generated using Swiss-Model [ 38] with the crystal structure of the eEF1A:eEF1Bα complex (PDB ID 1IJE, [ 8]) as the structural template.

The rational method features the functional approach and the structural template approach.

For target sequences with high sequence similarity to those of structure templates, the structural templates can be easily identified and the target sequences can be reliably aligned to the structural templates by those methods that use sequence information alone such as PSIBLAST [14] and HMMER [15].

The Vfold model predicts the 3D structure for a 2D structure based on the structural templates.

The distribution of the sequence identities associated with the structural templates used in modeling is shown in Figure 3. 60% of models are based on a template with a sequence identity greater than 30%, a common threshold for building reliable homology models.

A histogram of the number of sequences versus the sequence identity of the protein with the closest structural template in the dataset was plotted (Fig. 3).

In addition to the match to the core structural template, we also systematically documented all unique features of each newly-detected structure.