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 kinesin
and transducin examples, respectively.
data(kinesin)
data(transducin)
data(hivp)Three objects from analysis of the kinesin and transducin sequence and structure
data:
pdbs is a list of class pdbs containing aligned PDB
structure data. In the case of transducin this is the output of running
pdbaln on a set of 53 G[alpha]i structures from the PDB database (see pdbs$id
or annotation described below for details). The coordinates
are fitted onto the first structure based on "core" positions obtained from core.find and superposed using the function pdbfit.
core is a list of class "core" obtained by running the
function core.find on the pdbs object as described above.
annotation is a character matrix describing the nucleotide state and bound
ligand species for each structure in pdbs as obtained from the function pdb.annotate.
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.