Sentence examples for by a structure alignment from inspiring English sources

That is, given a set of training protein pairs and their reference alignments (built by a structure alignment tool), we maximize their occurring probability defined by Equation (2).

The ML method trains the CRF or CNF model parameters by maximizing the observed probability of a set of reference alignments built by a structure alignment tool.

The distance and contact restraints in the second-round TASSER are taken from the combination of the centroid structures and the PDB structures searched by the structure alignment program TM-align [ 40] based on the cluster centroids.

More pronounced topology-level improvements were achieved when new structural templates identified from the PDB were incorporated into the folding iterations; these templates were detected by the structure alignment program TM-align [ 6], which matches the TASSER models with each of the known proteins in the PDB to identify the templates that are structurally closest to the TASSER models.

However, we only use the first alignment generated by the structure alignment tools for a protein pair as the reference alignment.

The output of this procedure includes a "virtual structure alignment" produced by allowing the two domains of a DSCO pair to be independently rotated and translated and thus superimposed simultaneously.

Structures in each group were aligned by the multiple structure alignment function of RSmatch with default scoring matrices.

Such similarity is usually detected and quantified by protein structure alignment.

The TtPilF hexamer was constructed by secondary structure alignment in COOT [ 30] on to the co-ordinates of AfGspE from the thermophilic bacterium A. fulgidus ([ 18]; PDB accession 2OAP).

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.

Results: An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment.