2015
DOI: 10.4172/2167-0501.1000175
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The Hybrid Idea of (Energy Minimization) Optimization Methods Applied to Study PrionProtein Structures Focusing on the beta2-alpha2 Loop

Abstract: In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and their optimization methods used for energy minimization. To minimize a potential energy function, about 95% efforts are spent on the Lennard-Jones potential of van der Waals interactions; we also give a detailed review on some effective computational optimization methods in t… Show more

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Cited by 6 publications
(6 citation statements)
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“…The systems were energy minimized using the steepest descent algorithm to remove all atomic clashes. , This was followed by an equilibration under NVT conditions for 1 ns, where the reference temperature of 310 K was regulated with the velocity-rescale thermostat and the time constant was set to 0.1 ps. During minimization and initial equilibration stages, the heavy atoms of protein and lipids were subjected to position restraints with a force constant of 1000 kJ/mol· nm 2 .…”
Section: Methodsmentioning
confidence: 99%
“…The systems were energy minimized using the steepest descent algorithm to remove all atomic clashes. , This was followed by an equilibration under NVT conditions for 1 ns, where the reference temperature of 310 K was regulated with the velocity-rescale thermostat and the time constant was set to 0.1 ps. During minimization and initial equilibration stages, the heavy atoms of protein and lipids were subjected to position restraints with a force constant of 1000 kJ/mol· nm 2 .…”
Section: Methodsmentioning
confidence: 99%
“…The initial structures were placed in a cubic box; water molecules and 150 mM NaCl were added, and the systems were neutralized by inserting extra Na + ions. After that, the systems underwent energy minimization using the steepest descent algorithm to remove clashes between atoms, followed by two equilibration steps, each for 1 ns, under canonical ( NVT ) and isobaric–isothermic ( NPT ) ensemble conditions. During the equilibration, the pressure was kept at 1.0 bar using the Parrinello–Rahman pressure coupling method, , and the temperature was kept at 298 K using the velocity-rescale thermostat method .…”
Section: Experimental Sectionmentioning
confidence: 99%
“…The initial (already collapsed) monomer structures were solvated in a ∼2,000 nm 3 cubic box, including 150 mM Na + and Cl − ions and overall system neutralization, leading to about 200,000 atoms. The energy of each system was initially minimized using the steepest descent algorithm ( Müller and Brown, 1979 ; Zhang, 2015 ), followed by 1.0 ns equilibration and then the production runs under NPT ensemble conditions. The pressure and temperature were maintained at 1.0 bar and 298 K using the Parrinello-Rahman pressure coupling method ( Parrinello and Rahman, 1981 ; Parrinello and Rahman, 1982 ) and a velocity-rescale thermostat method ( Bussi et al, 2007 ), respectively.…”
Section: Methodsmentioning
confidence: 99%