194
S. Sakkiah et al.
Fig. 10.5 Overview of the MD simulation protocol
10.5.1 Initial Coordinates
The first step in an individual MD simulation is to select or obtain the 3D structure
of a protein or a protein complex. X-ray and nuclear magnetic resonance are the
two experimental techniques to determine 3D structures deposited in PDB. If the 3D
protein structure is not available in PDB, homology modeling can be used to construct
a 3D protein structure. The selection of the atomic representation of a protein is an
important step in MD because it can influence the dynamics simulation results.
S. Sakkiah et al.
Fig. 10.5 Overview of the MD simulation protocol
10.5.1 Initial Coordinates
The first step in an individual MD simulation is to select or obtain the 3D structure
of a protein or a protein complex. X-ray and nuclear magnetic resonance are the
two experimental techniques to determine 3D structures deposited in PDB. If the 3D
protein structure is not available in PDB, homology modeling can be used to construct
a 3D protein structure. The selection of the atomic representation of a protein is an
important step in MD because it can influence the dynamics simulation results.