Sentence examples for binding site is defined from inspiring English sources
In this study, an experimental binding site is defined as the geometric center of a ligand bound to the target protein, whereas the computationally predicted binding pocket center is obtained from eFindSite [9].
In contrast to a recently published approach where the entire binding site is defined by a Gaussian model for structure-based cross-reactivity predictions [4], PREDator employs only a few characteristic cavity-flanking amino acids [5] which are finally encoded in order to accelerate computations.
The "core" region of a binding site is defined as a contiguous stretch of nucleotides that is most important for TF-DNA binding.
The subsequence finally reported as containing the binding site is defined by the position of the two ends estimated from the distribution of the genomic positions of the fragment ends.
Since a binding site is defined based on the three dimensional structure of a molecule, it is difficult to identify a binding site with its structural formula alone, without stereo information [ 29].
In the Na+/H+ antiporters (Lee et al., 2013; Paulino et al., 2014) or the bile acid transporter ASBT (Zhou et al., 2014), where the binding site is defined by unwound stretches of two trans-membrane helices in a structurally homologous bundle, this process also involves a rotation of the bundle around a similar axis as in SeCitS, although the movement is significantly smaller.
Binding pockets of the two models were analyzed with SiteMap (version 3.7, Schrödinger, LLC, New York, NY, 2015): protein binding site was defined as the region within 10 Å from residue N93, thus the ECL2 region was excluded and the surface differences were due only to different conformations of residues in TM helices.
For each structure, the binding site was defined at 4Å around the co-crystallized ligand for the protomol generation step.
Like in previous work, the binding site was defined as those AAs that differed between the different mutants (a total of 24 residues) [28].
In GOLD, the binding site was defined as a sphere with a radius of 10 Å centered at the position of the Nε atom in residue Gln 257.
