Sentence examples for restraints based on the from inspiring English sources

Backbone dihedral angle restraints obtained using TALOS+ (Shen et al., 2009), as well as hydrogen-bond restraints based on the regular secondary structure patterns, were also incorporated into the structural refinement.

Several structure calculations were performed using ARIA with sets of distance restraints based on the solution and solid-state NMR experiments, as well as on the crystallographic structures.

Calculations were performed with two different distance restraints based on the conserved sulfate-binding sites: Ser65 was set to be within 10 Å (Cα-Cα) of either H302/R305 or K161/K211.

Additional distance restraints based on the observed coordination of the fucose O3 and O4 to the Ca2+ ion in other DC-SIGN or DC-SIGNR structures were also included.

Namely, loose restraints based on the cryo-ET maps (height = 10 ± 2 nm, width 26 ± 2 nm, inner radius = 8 ± 2 nm) were imposed to ensure the height and width of the assembly to be smaller than, respectively, 10 nm (maximum extension of YscD prior unfolding) and 24 nm (the PrgH rings features a width of about 27 nm).

In these cases, it is best to use the ideal guest molecule in order to assist in the modeling of the distorted molecules through soft restraints based on equivalent sets, such as the SADI and SAME commands in SHELXL, which make 1,2 and 1,3 bond distances equivalent within a specified standard deviation, thus not requiring the introduction of explicit bond distances or angles.

Distance restraints based on trNOESY data were used to constrain the conformation of the bound ligand.

The same procedure was applied to the refinement using difference restraints based on equation (3).

Here, we combine site-directed spin labeling, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations with novel energy restraints based on experimental electron paramagnetic resonance data to investigate the native transmembrane (TM) and periplasmic molecular architecture of closed MscS in a lipid bilayer.

In addition to commonly used restraints based on STD identification of ligand epitopes and chemical shift perturbation identification of residues in the binding pocket, simulation of STD build-up curves proved to be a useful way of scoring docked poses.

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