Detecting Local Symmetry Axis in 3-dimensional Virus Structures

He, J., Chiu, W., Ranjan, D., Schmid, M.F. and Jiang, W.

    This paper presents an efficient computational method to identify a local symmetry axis in 3-dimensional viral structures obtained using electron cryomicroscopy. Local symmetry is frequently observed in viral structures. Many virus structures have various types of local symmetry such as 2-fold, 3-fold and 6-fold that exist in certain limited regions on the 3-dimensional structure. Locations of local symmetry axes can be used in structure averaging as well as in detecting small structural variations among different copies of the same protein. We present a computational method that uses two-dimensional local correlation to identify the local symmetry axis in 3-dimensional viral structures. Instead of enumerating all the possible orientations of the symmetry axis, this method starts with a visually identified orientation and detects the trace of the axis, from which the exact orientation of the axis can be calculated. The complexity of this algorithm is analysed, and a comparison with a na•ve method is provided. This method is able to detect the symmetry axis fairly accurately if the initial orientation of the axis is within 20¡ from the z-axis, the viewing axis. The application of this method to herpes simplex virus B capsid structure obtained using electron cryomicroscopy technique is also presented.
Cite as: He, J., Chiu, W., Ranjan, D., Schmid, M.F. and Jiang, W. (2004). Detecting Local Symmetry Axis in 3-dimensional Virus Structures. In Proc. Second Asia-Pacific Bioinformatics Conference (APBC2004), Dunedin, New Zealand. CRPIT, 29. Chen, Y.-P. P., Ed. ACS. 265-270.
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