Molecular dynamics simulations of complexes consisting of proteins and nucleic acids

Author: Mgr. Vlastimil Zíma
Supervisor: RNDr. Ivan Barvík Jr., PhD.
Type: Bachelor

Abstract: This study summarizes basic information about nucleic acids and appropriate cellular processes. It also describes differences in behavior of viral nucleic acids, mainly in the case of HCV, HIV and SARS viruses. Then methods of computer physics - molecular dynamics and homology modelling, which have been used, are described. Finally products of application of these methods are demonstrated: molecular dynamic simulation of a simple system consisting of argon atoms, homology modeling and molecular dynamics simulations of SARS-CoV RdRp and HCV RdRp in the complex with a substrate.

Keywords: molecular dynamics, homology modelling, nucleic acids, HCV, SARS