Computational protocol: Moderate and strong static magnetic fields directly affect EGFR kinase domain orientation to inhibit cancer cell proliferation

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Protocol publication

[…] All of the Molecular Dynamics simulations were performed using the DL_POLY-4.0.7 program []. The initial heating and pre-equilibration (10 ns) were completed by Gromacs-4.5 molecular dynamic code []. The initial conformations of the EGFR were derived from the RCSB Protein Data Bank (code: 2GS6), and were protonated assuming a pH of 7.4 using the H++server (http://biophysics.cs.vt.edu). The protein and ions were described using AMBER03 force-field [] and the water molecules were described using TIP3P parameters []. The temperature was held at 310 K and pressure was maintained at 1 bar using a Nose '−Hoover coupling schemes. The integration step was set to 1fs. Simultaneously, to enhance the statistic sampling, three parallel MD simulations were carried out, final analysis for 10 ns trajectory of each MD simulation was performed using GROMACS tools, VMD [] and locally written code. The Shake method [] was used to keep all bonds and angles associating with hydrogen rigid at ideal values. In order to handle long-range electrostatic interactions, the smoothed particle mesh Ewald algorithm was used, with a cutoff length of 12 angstrom. The cutoff length for the Lennard-Jones potential was also set at 12 angstrom. […]

Pipeline specifications

Software tools GROMACS, AMBER, VMD
Application Protein structure analysis
Organisms Cricetulus griseus
Diseases Neoplasms, Genetic Diseases, Inborn