Sentence examples for atoms were added from inspiring English sources

Hydrogen atoms were added to each protein.

Missing atoms were added using the software VMD55 with the PSFGEN plugin.

Hydrogen atoms were added to each conformation before checking its structural integrity.

Then, all bonds in each enzyme were modified automatically and missing hydrogen atoms were added using Builder module in Insight II software package60.

Hydrogen atoms were added manually.

Hydrogen atoms were added using Chimera [21].

Non-polar hydrogen atoms were added by standard FlexX routines.

Hydrogen atoms were added to the pdb structures using AutoDockTools.

Hydrogen atoms were added in standard geometry and, where needed, with rotational optimization of OH, SH, and NH+3 positions.

Polar hydrogen atoms were added to the ligand and receptor.pdb files, and Gasteiger charges assigned.

Using the Biopolymer module, polar hydrogen atoms were added into the standard geometry.