Selected article for: "constant pressure and energy minimization"
Author: Lamborn, Ian T.; Jing, Huie; Zhang, Yu; Drutman, Scott B.; Abbott, Jordan K.; Munir, Shirin; Bade, Sangeeta; Murdock, Heardley M.; Santos, Celia P.; Brock, Linda G.; Masutani, Evan; Fordjour, Emmanuel Y.; McElwee, Joshua J.; Hughes, Jason D.; Nichols, Dave P.; Belkadi, Aziz; Oler, Andrew J.; Happel, Corinne S.; Matthews, Helen F.; Abel, Laurent; Collins, Peter L.; Subbarao, Kanta; Gelfand, Erwin W.; Ciancanelli, Michael J.; Casanova, Jean-Laurent; Su, Helen C.
Title: Recurrent rhinovirus infections in a child with inherited MDA5 deficiency
  • Document date: 2017_7_3
    • ID: vipx6t7e_27
    Snippet: Molecular dynamics simulations were performed using the Assisted Model Building with Energy Refinement (AMB ER14) simulation package (Case et al., 2015) with GPU acceleration (Salomon-Ferrer et al., 2013) . The FF99SB all-atom potential (Hornak et al., 2006) was used along with parameters for ATP (Meagher et al., 2003) and Zn 2+ (Li et al., 2013) . Starting with the crystal structure of MDA5 (Protein Data Bank ID 4GL2; Wu et al., 2013) , ANP was .....
    Document: Molecular dynamics simulations were performed using the Assisted Model Building with Energy Refinement (AMB ER14) simulation package (Case et al., 2015) with GPU acceleration (Salomon-Ferrer et al., 2013) . The FF99SB all-atom potential (Hornak et al., 2006) was used along with parameters for ATP (Meagher et al., 2003) and Zn 2+ (Li et al., 2013) . Starting with the crystal structure of MDA5 (Protein Data Bank ID 4GL2; Wu et al., 2013) , ANP was changed to ATP and lysine at position 365 was mutated to glutamic acid in PyMol (The PyMol Molecular Graphics System, Version 1.7.2.1; Schrödinger, LLC). The system was protonated in tleap, solvated with TIP3P explicit water in a periodic truncated octahedron extending 10A beyond the MDA5 complex, neutralized with Na + , and brought to ∼150 mM of sodium chloride by randomly exchanging solvent molecules with Na + or Cl − . The system was then subjected to energy minimization with diminishing harmonic restraints, followed by heating from 100K to 303K over 30 ps at constant volume with a Berendsen thermostat. Production runs were generated by switching the heated system to a constant pressure and temperature ensemble and allowing the system to equilibrate over 120 ps. All simulations were run in triplicate using the SHA KE algorithm.

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