Sentence examples for the selected conformation from inspiring English sources

Our results suggest that the force fields, the protein flexibility, and the selected conformation of the binding site substantially influence the correlation coefficient, while the sampling strategies and ensemble docking only mildly affect the prediction accuracy.

K-mean clustering method was used to generate the ligand perturbation ensemble and similar/redundant conformations (rmsd to the selected conformation is less than 0.5 Å) were omitted.

These calculations are repeated for increasing weights of the selected conformation, until it becomes impossible to find an ensemble in agreement with the experimental data, thus determining the MaxOcc value of that conformation.

The LSTa AV18 complex was built by superimposing a previously selected conformation of LSTa on the LSTa-like trisaccharides cocrystallized with H1 (A/Puerto Rico/8/34 H1N1) with amino acids within the binding site typical of an avian HA (PDB entry 1RVX).

The final selected conformations of docked cholesterol were chosen based on a cluster analysis of all the 50 conformations using a 0.5 Å cutoff.

The α,β-double bond constricts the topography of the side chain and limits the position of the β-substituents, which leads to the appearance of isomers Z and E. Furthermore, possible co-planarity of the α,β-double bond and flanking amide groups enable π-electron conjugation, which should be considered as a stabilising force of selected conformations.

However, in the MOE preparation, the selected pyrrolidine conformation is different and led to an obvious deviation in the placement of enalaprilat's carboxylate group, thus, making close contacts with the surrounding polar residues infeasible.

The process concluded when the binding poses and energies of the selected peptide conformation stabilized over 5 iterations.

positioning the selected ligand conformation into the binding site, and (4) rigid body energy minimization of the candidate ligand pose/conformation using the DockScore energy function and updating the saved list of ligands with the candidate pose.

The existence of the bioactive conformer supports evaluation of correct conformation of the automatically selected conformers.

Unrestrained molecular dynamics simulations explore binding conformations close to each other, hence the docking poses obtained were clustered by root mean square deviation (RMSD) in order to avoid selecting conformations that interconvert during the simulations time scales.