TCB Publications - Abstract

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 Discussion, 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.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: Journal, Request a Copy