Article

Parallel computing strategies for determining viral capsid structure by cryoelectron microscopy

US Nat. Inst. of Health
IEEE Computational Science and Engineering 05/1998; DOI: 10.1109/99.683745
Source: IEEE Xplore

ABSTRACT To calculate a full 3D structural model of a virus capsid,
researchers analyzed cryoelectron micrographs that contain many randomly
oriented images of the views. The authors use parallel computing
techniques to improve the performance of the computational algorithms
that determine each particle's orientation and generate the 3D model.
This enhanced computational performance allows analysis of many more
particles and a more precise determination of their orientations,
letting researchers study important details of virus capsids at higher
resolutions

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    • "High performance computing implementations are described in Refs. [11] [12] [13]. Once the projection orientations are determined, the reconstruction problem is large (since it is in 3-D) but tractable. "
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    ABSTRACT: Statistical methods for computing multiple 3-D reconstructions from cryo electron microscope images (noisy 2-D projections in unknown orientations) of mixtures of assembly mutants of Cowpea Chlorotic Mottle virus are described.
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    • "High performance computing implementations are described in Refs. [11] [12] [13]. Once the projection orientations are determined, the reconstruction problem is large (since it is in 3-D) but tractable. "
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    ABSTRACT: The D reconstruction of the electron scattering intensity of a virus from cryo electron microscopy is essentially a 3D tomography problem in which the orientation of the 2D projections is unknown. Many biological problems concern mixtures of different types of virus particles or mixtures of different maturation states of the same type of virus particle. For a variety of reasons, especially low SNR, it can be very challenging to label the type or state shown in an individual image. Algorithms capable of computing multiple reconstructions, one for each type or state, based on images which are not labeled according to type or state, are described and demonstrated on experimental images.
    Acoustics, Speech, and Signal Processing, 1988. ICASSP-88., 1988 International Conference on 01/2005; 5. DOI:10.1109/ICASSP.2005.1416436 · 4.63 Impact Factor
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    • "This kind of definition of good orientations suggests an Expectation Maximization-type procedure of repeatedly finding the best model for fixed orientations and the best orientations for a fixed model, see e.g. [3] [11] [20] [22] [30]. Due to the strong dependency on the reconstruction method, it is not easy to say analytically much (even whether it converges) about this approach in general. "
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    ABSTRACT: In this report we study the problem of determining three-dimensional orientations for noisy projections of randomly oriented identical particles. The problem is of central importance in the tomographic reconstruction of the density map of macromolecular complexes from electron microscope images and it has been studied intensively for more than 30 years. We analyze the computational complexity of the orientation problem and show that while several variants of the problem are $NP$-hard, inapproximable and fixed-parameter intractable, some restrictions are polynomial-time approximable within a constant factor or even solvable in logarithmic space. The orientation search problem is formalized as a constrained line arrangement problem that is of independent interest. The negative complexity results give a partial justification for the heuristic methods used in orientation search, and the positive complexity results on the orientation search have some positive implications also to the problem of finding functionally analogous genes. A preliminary version ``The Computational Complexity of Orientation Search in Cryo-Electron Microscopy'' appeared in Proc. ICCS 2004, LNCS 3036, pp. 231--238. Springer-Verlag 2004.
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