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- W216009940 abstract "In order to introduce disulfide bond to a protein certain pair residues need to be mutated to cysteine. To find the best candidate for mutation computational web server (disulfide by design server) is used then PyMol software is used to mutate proposed residues. Followed that molecular dynamic simulation is run in Gromacs package in following seven steps; mutated PDB files need to be readable for Gromacs therefore a tool named pdb2gmx is used to convert PDB to topology file readable by Gromacs (Topology generation), then an aquatic environment need to be defined (box and solvent define), in order to neutralize the system ions need to be added to system (adding ion), in order to brings atoms in the correct position energy minimization need to be perform (energy minimization), then the temperature and pressure of the system need to be equilibrated (equilibration), after these steps system is ready to be simulated for defined time (MD production) and finally analyzing the MD product trajectory files by using Root-Mean square division (RMSD), Root-Mean square fluctuation (RMSF) radius of gyration (RG) calculations (analysis)." @default.
- W216009940 created "2016-06-24" @default.
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- W216009940 date "2015-01-01" @default.
- W216009940 modified "2023-10-14" @default.
- W216009940 title "Methodology of Mutant Creation and Molecular Dynamic Simulation" @default.
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- W216009940 doi "https://doi.org/10.1007/978-981-287-432-0_3" @default.
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