Sentence examples for binding pocket defined by from inspiring English sources
The molecules were first docked by the FRED algorithm (McGann, 2012) of the OpenEye suite into the binding pocket defined by TRPV1 cryo-EM structures, with the constraints of experimentally derived electron density maps of the two ligands.
Similar to the structure of murine BRDT(1) (Morinière et al., 2009), human BRDT(1) exhibits the canonical structural features of a bromodomain, namely a left-handed bundle of four antiparallel α helices (αZ, αA, αB, and αC) and a hydrophobic acetyl-lysine binding pocket defined by interhelical ZA and BC loops (Dhalluin et al., 1999).
22 They found that the length of the binding pocket, defined as the distance between Ser5.42 and Asn7.39, is contracted by 1 Å with an agonist bound relative to when an antagonist is bound.
They demonstrated that, when the protein structure and the general location of ligand binding pocket are defined (by cryo-EM or other structural biology approaches), modern computational tools are able to accurately identify correct binding configuration of the ligand.
The binding pocket is defined by amino acids within 3.5 Å of the D1 receptor agonist doxanthrine, which was used as environment 2 during the homology modeling procedure.
The binding pocket is defined by amino acids within 3.5 Å from the D2 receptor agonist - R -2-OH-NPA, 32 which was used as environment 3 for induced fit during the homology modeling procedure.
Tournamille et al. found that a chemokine-binding pocket was defined by the close proximity of the first and fourth transmembrane domains of the DBG/DARC protein and also by the importance of the N-terminal extracellular region correlated to chemokines binding to the DBG protein [ 19, 20].
Alterations include four ligand binding pocket mutations defining sites of inhibitor binding and four variants conferring constitutive activity and inhibitor resistance, illuminating pivotal residues that ensure receptor autoinhibition.
