engleski

Glimpses of biomolecular structure and dynamics through worldwide distributed computing: from protein folding to structure determination

Currently, the only method to study proteins and other biomolecules on a single molecule level with femtosecond time resolution is through computer simulations. However, the field of classical molecular dynamics simulations of biomolecules has traditionally been haunted by three principal challenges. One, there is a challenge of representation – how do we represent molecules in silico? Two, there is a challenge of sampling - given a model, how do we sample the phase space quickly and accurately? Finally, there is a challenge of correspondence with reality - how do we properly link the simulation results with experiments? In this talk, I will give three examples which to different extents address all three of these challenges. In particular, I will focus on the development and usage of the Folding@Home distributed computing network, which currently numbers more than 250, 000 processors all over the world, in addressing basic questions of protein folding and dynamics. Specifically, I will discuss some results regarding the folding mechanism and folding rates of ultrafast-folding proteins, as well as the structure of the unfolded state of proteins. In addition, I will focus on some of the recent results concerning the issues of conformational averaging in scattering techniques.

distributed computing; Folding@Home; molecular dynamics

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