A new program library
named “CAPLIB” was developed for the modeling and analysis
of icosahedrally symmetric virus capsids. CAPLIB is equipped with
the mathematical data of 60 rotation matrices of icosahedral symmetry,
15 planes bisecting the entire capsid structure, and a table summarizing
how the 60 asymmetric units (cells) are partitioned by the planes.
CAPLIB contains the function to determine the cell numbers of atoms
from the atomic positions and the function to determine the rotation
axes and angles from the rotation matrices. Using CAPLIB, it is possible
to generate the structure of any selected protein unit within the
entire capsid by rotating a single protein unit structure. CAPLIB
can classify Protein Data Bank files of capsids with the directions
of rotation axes, rotate the protein structure onto the standard position,
and perform various deformations of the entire capsid. The interface
to the molecular graphics software, PyMOL, was also developed for
efficient modeling of capsids.
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