It is possible to perform a structural alignment on structures produced by structure prediction methods.
The key difference in our application is the consideration of alignment with various structural alterations and their effect of fragment directionality.
Vorolign compares two protein structures and produces a structural alignment of the two structures and an associated alignment score.
The two family alignments were aligned using a structural alignment of the two protein structures.
Three structural alignment methods employing various conformers were used to scrutinize the effect of conformation selection on the predictive accuracy of QSAR models.
In order to show the occurrence of HGT and its origin, a general gene tree of glycosyl hydrolases of the GH13 family, which have a broad activity range [ 58], from various organisms was built from a structural alignment as described in ref. [ 59], adding the sequences studied here.
Found homologous structures are subsequently aligned with the target protein by a global structural alignment algorithm.
SARST [34] is an extremely rapid protein structural alignment search method which describes protein structures as one-dimensional structural strings and recruits BLAST as its alignment engine.
The information on miRNA families has been derived from Rfam database, in which various kinds of RNAs are classified into families based on their sequence and structural alignment [ 36].
Duplicated domains within a structure were defined by manual observation and sequence and structural alignment.
Alignment based methods can be further divided into sequence alignment based and structural alignment based methods.
