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AbstractProtein folding has been one of the biggest issues in
structural biology during the years. Many folding mechanisms
have been proposed to explain why protein molecules fold so fast
when little time is given. However, formatting such kind of
theory requires many calculations and is very CPU-intensive,
usually supercomputers are involved. To get ride of this
limitation, we develop a fast calculation routine which can be
run on a personal workstation, and yield satisfying results.
Simplified protein model, which we are using, cuts off the atom
number participated in simulation, while still giving physical
meaning for the structure. In this model, side chain atoms are
reduced to a single sphere having the same mass and charge and
then go through the entire molecular dynamics simulation.
Afterwards, complete side chain configuration was restored and
give the complete energy of the structure status. With this
manipulation, unfolding simulation can be conducted within a
week. This procedure is easy to be implemented and worth further
development.
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