Classical molecular dynamics is the simulation of chemicals using the simplest atomistic model where each atom is a tiny mass with a charge interconnected with spring-like bonds. Faster computers and better simulation algorithms mean that it is now possible to run classical molecular dynamics simulations of biochemical systems with up to millions of atoms for microseconds of simulation time. In my research group, we perform such simulations to answer biochemical questions about protein and nucleic acid systems that are highly flexible. These include viral chemokine inhibitors that have flexible loops that change structure when binding to their target molecules and DNA-binding anticancer drugs whose preferred binding structure involves contorting the shape of DNA.
Chemistry and Chemical Biology
Classical molecular dynamics simulations of flexible proteins and nucleic acids.
QSB Emphasis Areas:
Molecular Systems Biology
Quantitative and Theoretical Biology