Sentence examples for binding poses of the from inspiring English sources

The crystallographic binding position coincided with two free energy minima, which reflects the two possible binding poses of the TDG disaccharide.

Analysis of the inhibition data by proteochemometric modeling suggested the possibility for different binding poses of the shortened peptides compared to the octapeptides, which was supported by results of docking of WYCW-NH2 into the X-ray structure of DEN-3 protease.

Docking into the P2Y14R model based on the P2Y12R– 34 template did not result in high-score binding poses of the ligand, even when side chain flexibility of the receptor was taken into account.

In this work, we produced and used SDM data, homology modeling followed by MD simulation, and ensemble-flexible docking to generate binding poses of the Orexin peptides in the OX receptors to rationalize the SDM data.

The reasons for the nonproductive poses of the tetrahedral intermediate formed from N-formimino- l-aspartate are not immediately clear; this compound is not a substrate for Pa5106 and the unproductive binding poses of the substrate and tetrahedral intermediates may explain why this compound is not a substrate for Pa5106.

Binding poses of the compounds were energetically favorable and showed good interactions with active site residues.

Here we present the binding poses of these two compounds which fulfill our criteria of ligand selection (i.e., (1) steric complementarity between pocket and ligand, (2) presence of cation π interactions, and (3) preferably occurrence of hydrogen bonds).

The conformational transformation may depend on the functional group and binding pose of the ligand, giving the binding pocket greater flexibility and accordingly allowing for an induced fit of the enzyme-ligand binding site around the newly introduced ligand.

These interesting results are also in agreement with docking experiments suggesting a good binding pose of the synthesized compounds into the pocket of the oxidase enzymes, in particular of MAO-B.

Molecular modeling performed using two different approaches – FLAP and Amber software – shows that in the binding pose of the newly synthesized compounds as compared with the crystallographic pose of linezolid, the 1,2,4-oxadiazole moiety seems to perfectly mimic the function of the morpholinic ring, since the H-bond interaction with U2585 is retained.

In addition, the electrostatic potential binding energy and similarity between the binding sites can be calculated based on the binding pose of the ligand.