Abstract
Complex of Renin protein with three ligands (EMBOSS_2737, EMBOSS_155075, and EMBOSS_11556) along with its main ligand, Aliskiren, is simulated using Molecular Dynamics (MD) approach for a 100 ns period. Preprocessing steps of preparation of protein, ligand, and the complex topology are carried on so the complex is solvated in a cubic simulation box, full of SPC/E water molecules as the solvent, with same molecular concentration as its ligand. Optimization of energy, in terms of Energy Minimization, and temperature and pressure equilibriums are also conducted, to make sure the system is suitable for the simulation. Finally, the MD process is simulated, suggesting the EMBOSS_2737 as the most specific ligand to the protein and showing minimal RMSD, in the 300 K environment.
This project is carried on at Bioinformatics Camp (BioinfCamp), with the help of projects team, and under the supervision of Mr. Roohparvar.
