Sentence examples for bonds were assigned using from inspiring English sources
Hydrogen bonds were assigned using HBPLUS.
Partial atomic charges were assigned to CTN06 using the Gasteiger-Marsili method, and, after the merging of non-polar hydrogens, rotatable bonds were assigned using Autodock Tools.
All the heteroatoms coupled with proteins including water molecules, bound ligands and any co-crystallized solvent were discarded from the PDB file and the missing assignments like proper bonds, bond orders, hybridization and charges were assigned using the Molegro Virtual Viewer [40].
Heterostate for cocrystallized ligand was generated using Epik; protonation state and optimization of H-bonding of the protein side chains were assigned using ProtAssign.
The proteins were prepared by using the Protein Preparation Wizard, pre-processed and heterostate for co-crystallized ligand was generated using Epik; protonation state and optimization of H bonding of the protein side chains were assigned using Protassign, energy minimization (impref minimization) was carried out using default constraint of 0.3 Å RMSD and OPLS 2005 force field.
All possible rotatable bonds and partial atomic charges (Gasteiger-Marsili formalism) of the ligands, as well as the Kollman charges for all atoms of the enzyme, were assigned using the AutoDock tool 1.5.4, a program included in AutoDock [ 37].
Cohesion of the wet sandy soil was assigned using a parallel bond contact model, where the normal and shear stiffness of the bond, the normal and shear strength, and the size of the connecting geometry were the main parameters.
Hydrogen bonds were assigned based on analysis of NOEs and secondary structure predictions by CSI [56] and TALOS [55].
