John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten.
GPU-accelerated analysis and visualization of large structures
solved by molecular dynamics flexible fitting.
Faraday Discussions, 169:265-283, 2014.
(PMC: PMC4208074)
STON2014
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray
crystallography with molecular dynamics simulations for the determination of all-atom
structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from
hybrid fitting is computationally demanding, particularly in the context of a multiplicity of
structural conformations that must be evaluated. Existing tools for quality-of-fit analysis
and visualization have previously targeted small structures and are too slow to be used
interactively for large biomolecular complexes of particular interest today such as viruses
or for long molecular dynamics trajectories as they arise in protein folding. We present new
data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-
of-fit metrics linking all-atom structures and molecular dynamics trajectories to
experimentally determined density maps obtained from cryo-electron microscopy or X-ray
crystallography. We evaluate the performance and accuracy of the new quality-of-fit
analysis algorithms vis-a-vis existing tools, examine algorithm performance on GPU-
accelerated desktop workstations and supercomputers, and describe new visualization
techniques for results of hybrid structure fitting methods.
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