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Biophys J. 1998 Jan;74(1):576-88.

Refinement of herpesvirus B-capsid structure on parallel supercomputers.

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1
Texas Center for Advanced Molecular Computation, University of Houston, 77204-3476, USA.

Abstract

Electron cryomicroscopy and icosahedral reconstruction are used to obtain the three-dimensional structure of the 1250-A-diameter herpesvirus B-capsid. The centers and orientations of particles in focal pairs of 400-kV, spot-scan micrographs are determined and iteratively refined by common-lines-based local and global refinement procedures. We describe the rationale behind choosing shared-memory multiprocessor computers for executing the global refinement, which is the most computationally intensive step in the reconstruction procedure. This refinement has been implemented on three different shared-memory supercomputers. The speedup and efficiency are evaluated by using test data sets with different numbers of particles and processors. Using this parallel refinement program, we refine the herpesvirus B-capsid from 355-particle images to 13-A resolution. The map shows new structural features and interactions of the protein subunits in the three distinct morphological units: penton, hexon, and triplex of this T = 16 icosahedral particle.

PMID:
9449358
PMCID:
PMC1299410
DOI:
10.1016/S0006-3495(98)77816-6
[Indexed for MEDLINE]
Free PMC Article
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