data(kinesin) data(transducin) data(hivp)
These data sets contain the results of running various Bio3D functions on example kinesin and transducin structural data, and on a short coarse-grained MD simulation data for HIV protease. The main purpose of including this data (which may be generated by the user by following the extended examples documented within the various Bio3D functions) is to speed up example execution. It should allow users to more quickly appreciate the capabilities of functions that would otherwise require raw data download, input and processing before execution.
Note that related datasets formed the basis of
the work described in (Grant, 2007) and (Yao & Grant, 2013) for
transducin examples, respectively.
Three objects from analysis of the
transducin sequence and structure
pdbscontaining aligned PDB structure data. In the case of transducin this is the output of running
pdbalnon a set of 53 G[alpha]i structures from the PDB database (see
annotationdescribed below for details). The coordinates are fitted onto the first structure based on
"core"positions obtained from
core.findand superposed using the function
"core"obtained by running the function
pdbsobject as described above.
pdbsas obtained from the function
One object named
net in the hivp example data stores the correlation
network obtained from the analysis of the MD simulation trajectory of HIV
protease using the
cna function. The original trajectory file can be
accessed by the command system.file("examples/hivp.dcd", package="bio3d").
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Grant, B.J. et al. (2007) J. Mol. Biol. 368, 1231--1248.
Yao, X.Q. et al. (2013) Biophys. J. 105, L08--L10.