Sentence examples for site alignment from inspiring English sources
Afterwards, the resulting structures are being aligned with our new active site alignment algorithm ASCONA [2] which has been developed with a focus on an accurate detection of protein backbone variations.
Furthermore, it also includes structural bioinformatics solutions for inverse screening, binding site alignment, and searching interaction patterns across structure libraries.
When a binding site alignment was performed (using all residues within 5 Å of abacavir), the measured RMSD was less than 0.4 Å for all three crystal structures, which is excellent.
In this approach, bioisosteric replacements are identified using local binding site alignment algorithm ProBiS [15 19], which enables identification of locally similar binding sites irrespective of proteins' folds or amino acid sequences.
Based on the active site alignment, a further step detects flexible regions within the binding site and uses a remaining rigid core for a superimposition of the generated ensemble.
The Laj applet [ 29] was then used for visualization for Fig. 2 and for the web site alignment tool.
To extend the repertoire of methods for obtaining bioisosteric and scaffold replacements, we developed a freely available pre-calculated database of bioisostere replaceable fragments obtained with a rigorous all-against-all PDB local binding site alignments.
In contrast to an agreed upon mechanistic understanding of self-cleavage by Rzb hammerhead and pistol ribozymes, there exists a divergence of views as to the cleavage site alignments and catalytic mechanisms adopted by twister and twister sister ribozymes.
This review focuses on recent structure function research on active site alignments and catalytic mechanisms of the Rzb hammerhead ribozyme, as well as newly-identified pistol, twister and twister sister ribozymes.
We first created the PFM for each of the 124 binding site alignments.
Our program supports two methods to estimate a rate factor for each site: Alignment-Based rate factor α (α AB ) and Maximum Likelihood-estimated rate factor α (α ML ).
