Selected article for: "binding site and helicase site"
Author: Deepak Kumar; Nitin Sharma; Murali Aarthy; Sanjeev Singh; Rajanish Giri
Title: Mechanistic insights into Zika virus NS3 helicase inhibition by Epigallocatechin-3-gallate: Supplementary Files
  • Document date: 2019_1_26
    • ID: k11iupe0_36
    Snippet: Molecular dynamics simulation was executed for the apoprotein and complex of ZIKA helicase with the EGCG at NTPase site and RNA binding site using the Desmond module implemented in Schrodinger(a). The OPLS-AA (Optimized Potentials for Liquid Simulations -All Atom) 2005 force field was used for the minimization of the complex and apoprotein (40) . The structures of the protein and complex were imported in the Desmond setup wizard and were solvated.....
    Document: Molecular dynamics simulation was executed for the apoprotein and complex of ZIKA helicase with the EGCG at NTPase site and RNA binding site using the Desmond module implemented in Schrodinger(a). The OPLS-AA (Optimized Potentials for Liquid Simulations -All Atom) 2005 force field was used for the minimization of the complex and apoprotein (40) . The structures of the protein and complex were imported in the Desmond setup wizard and were solvated in a cubic periodic box of TIP3P water molecules. The structures were neutralized by adding a suitable number of counter ions and 0.15 M of salt concentration (41) . Steepest descent, a hybrid method is implemented for the local energy minimization of the system. The limited memory

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