Sentence examples for by aligning the binding from inspiring English sources
For instance, an interface prediction and classification system, Prism, defines structural similarity by aligning the binding sites that form each interface using MultiProt software [18].
The occupancy pattern of Htz1 (or Nap1) around special sites (such as TSSs, REG sites and TTSs) is represented with average binding ratio (log2) by aligning the binding profile for each gene at the special site.
To understand the organizations of Htz1 and Nap1 at promoters, we calculated the average binding ratio profiles for Htz1 and Nap1 by aligning the binding profiles for 5419 yeast genes at TSSs.
I2I-SiteEngine compares interfaces by aligning the functional groups at binding sites, instead of aligning molecular interactions within the interface like Galinter.
Before amplification, newly designed primers (supplementary table S7, Supplementary Material online) were tested in silico for unique binding by aligning the forward and reverse sequences against the scaffolds of the polar bear assembly using BLASTn.
Images were generated by aligning the Coh domain (gray) from PDB 2CCL (green, binding mode (A ) and 1OHZ (red, binding mode (B ) using the VMD plugin MultiSeq (Humphrey et al., 1996 ; Roberts et al., 2006 ).
The monomeric model was subsequently aligned on the dimeric assembly of the 4FBW template to generate a dimer, and the approximate position of DNA binding was determined by aligning the P. furiosus structure containing dsDNA (PDB code: 3DSC) with the dimeric model.
A putative AmrZ binding site was also observed by aligning the 154 regions with the MEME software.
The primer binding site (PBS) was identified by aligning the sequence downstream of the 5′ long terminal repeat (LTR) to that of 3′ regions of tRNAs.
We next determined the primary binding profiles for each protein by aligning the enriched sequences to a seed sequence, and calculating a position weight matrix (PWM) using the background corrected multinomial method as described previously (Jolma et al., 2010, 2013).
For the carbohydrate-binding module, the location of the beta strands was inferred by aligning the sequences to a CBM from an endoglucanase from Cellulomonas fimi (1EXG).
