Sentence examples for modelled structure from inspiring English sources

Sequence alignment and structural superimposition of a modelled structure of DUF1572 (UniProt: Q5L211_GEOKA) with YfiT from Bacillus subtilis (PDB ID: 1RXQ [ 35]) as template, reveals the conservation of histidine residues that can potentially coordinate a metal-ion (Fig.  5a).

However, these results are specific to the modelled structure and the input parameter set.

The modelled structure of the Bgl1 predicts the 8 barrel type structure with deep and narrow active site, whereas, Bgl3 shows the 8 barrel and 6 sandwich structure with shallow and open active site.

Furthermore and similarly to the structure of the TMD_I, the hydrogen bond network connecting Asp4602.50 of the 455-NLxxxD-460 motif in TM2 with Met6376.48 of the 636-CMxP-639 motif in TM6 is not observed in the modelled structure of the TMD_In.

Based on the structure of its donor substrate, UDP-N-acetyl-glucosamine, as well as the modelled structure of the bacterial chitin synthase NodC, we designed a novel scaffold which was then further optimized into a series of chitin synthase inhibitors.

The stereochemical quality of the modelled structure was analysed using procheck [36].

A phenetic analysis of RMSD distances obtained by superposition of the modelled structures revealed that structural variability in the TIR domain of all three receptors was lower than ECD variability (see Additional file 2: Figures S4d, S4e and S4f).

For all the 3D modelled structures, a set of structural properties were computed, including: i) the Druggability Score (DS) for each pocket, ii) the active site residues (if available) according to the template structures, iii) the conserved or family relevant residues.

The VADAR web-server was used to predict the structural parameters of the modelled structures [47] (http://redpoll.pharmacy.ualberta.ca/vadar/).ualberta.ca/vadar/

On the other hand, the SNP effects on protein functions were inferred by modelled structures because the molecular modelling method has been found useful for estimating the effects of the substitution of amino acid residues on protein function.

Models with the highest C-scores and conformation similarities to other modelled structures were used for further analysis.