High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
Figure 6
System for MD simulation of trypsin.
The protein is shown by the space-filled model, and the ligand is colored blue. The peripheral residues around the active center (red region), a ligand, and water molecules were allowed to move in the MD simulation. The protein residues (grey) were restrained to the X-ray structure by a harmonic energy term. Similar systems were used for the other target proteins.