Workshop on Molecular Visualisation, Modelling and Dynamics
Welcome to a workshop on molecular visualisation, modelling and dynamics. In this workshop you will learn how to use molecular visualisation and dynamics software to view, model and build biomolecular systems.
Molecular dynamics simulations provide a computational microscope that lets you watch how a molecule moves over time. Molecular dynamics lets you zoom in and view how molecules move and vibrate at the atomic level. For applications in synthetic biology and biochemistry, molecular dynamics allows you to watch how proteins and other biomolecular molecules move and interact. This can provide you with a greater understanding of the interactions and behaviour of biomolecules.
This workshop is based on the science described in this paper. This paper describes a set of simulations that were performed to predict whether or not the existing flu drugs (oseltamivir - also called Tamiflu, zanamivir - also called Relenza, and peramivir) would still be effective against the new H7N9 strain of flu that appeared in China in 2013. These flu drugs work by targetting a protein called neuraminidase. The paper describes how molecular models of the neuraminidase protein in H7N9 influenza were built, and then how they were visualised to understand how mutations in the protein affected binding of the drugs. Molecular dynamics simulations were then performed that modelled how the atoms in the drugs and protein moved. In effect, these simulations provided a computational microscope that allowed us to zoom in and view exactly how the drugs bound to the protein. Computational screening simulations were then conducted that involved the modellers performing point mutations on the protein and then viewing how these mutations affected drug binding during molecular dynamics simulations. These simulations provided the first insight into how an emerging mutant strain of H7N9 influenza was likely to show resistance to oseltamivir.
This workshop is divided into three parts;
- Part 1: Molecular Visualisation : Visualisation of biomolecules
- Part 2: Molecular Dynamics : Theory and practice of running molecular dynamics simulations
- Part 3: Mutation Studies : How to set up a protein simulation, including how to perform point mutations
These three parts are self-guided and allow you to go at your own pace. It is anticipated that part 1 will take about 2 hours, while parts 2 and 3 will take about 90 minutes each.
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