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In Silico Design of Alkhumra Virus NS3 Protease Inhibitors
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Jurica Novak Molecular dynamics (MD) simulations were performed using AMBER22 to model the NS3 protease with and without the NS2B cofactor. The simulation protocol followed a prior study, with an extended 1000 ns production run. Systems were subjected to two-step energy minimization: first, 10,000 cycles with positional restraints (10.0 kcal mol Å) on the protein, followed by unrestrained minimization. Equilibration involved gradual heating to 310 K over 500 ps (NVT), followed by 1000 ns production...
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