kinesin {bio3d} | R Documentation |
These data sets contain the results of running various bio3d functions on example data. 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 input and processing before execution.
data(kinesin)
Five objects from analysis of the kinesin
sequence and structure
data:
ali
, a character
alignment matrix, and id
, a character vector of ids/names.
This is the output of running read.fasta
on
the example alignment “kinesin_xray.fa”. "3dalign"
containing aligned PDB
structure data. This is the output of running
read.fasta.pdb
with the aln
object. "core"
obtained by running the
function core.find
on the pdbs
object.fit.xyz
on the
pdbs
object, using the “core atom indices”
contained in core
. pca.xyz
on the “core fitted
coordinates” contained in the xyz
object. dssp
FASTA alignment and PDB structure data from the bio3d “example” directory. A related but more extensive dataset formed the basis of the work described in (Grant, 2007).
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. Grant, B.J. et al. (2007) J. Mol. Biol. 368, 1231–1248.