Sentence examples for binding site we considered from inspiring English sources
For interactions with more than one experimentally verified binding site, we considered the one ranked highest (according to their predicted free energy) for each method.
To restrict the selection of non-functional binding sites we considered only the binding sites occurring in the optimized functional window (-7 to 0) of the promoter sequences (see above).
When we compute the fitness (IC score) of a motif given all the binding sites, we consider all columns, because in this case we have all the information to derive a PWM.
Although multiple regulatory proteins can also form a complex and the complex can regulate a target gene via a single binding site, we only consider regulation via multiple binding sites, the single binding site case being similar with our previous analysis.
Given this vector, when calculating the match score between a consensus and a potential binding site, we only consider the positions with 1's.
Quality of binding site predictions: we considered the scoring methods employed by Targetscan due to their solid statistical approach [28].
(3) Quality of binding site predictions: we considered the scoring methods employed by Targetscan due to their solid statistical approach [28].
The molecules with a maximum of at least 2 H-bonds with the hinge region at the ATP binding site were considered along with any one of the rings.
Three properties of the binding site were considered: the total number of atoms at 4 Å from its surface, its hydrophobicity, i.e., the fraction of carbon atoms among this total number, and its exposure to the solvent.
Only genes containing both a potential core binding site and a potential half binding site were considered as positive for the presence of a "complete QRE".
