Sentence examples for binding site was defined from inspiring English sources

For each structure, the binding site was defined at 4Å around the co-crystallized ligand for the protomol generation step.

The binding site was defined on the basis of used reference ligands with a radius of 10 Å.

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 atom C14 in the bound ligand.

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.

In GOLD, the binding site was defined as a sphere with a radius of 10 Å centered at the position of atom C6 in the bound sialic acid ligand.

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].

For GOLD (version 5.1) docking, residues of the binding site were defined by specifying the crystal structure ligand coordinates and using a cutoff radius of 10 Å, with the 'detect cavity' option enabled.

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.

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].