kinesin {bio3d}R Documentation

Bio3d Example Data

Description

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.

Usage

data(kinesin)

Format

Five objects from analysis of the kinesin sequence and structure data:

    aln
    is a list with two components: 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”.
    pdbs
    is a list of class "3dalign" containing aligned PDB structure data. This is the output of running read.fasta.pdb with the aln object.
    core
    is a list of class "core" obtained by running the function core.find on the pdbs object.
    xyz
    is a numeric matrix of “core fitted coordinates” obtained by running the function fit.xyz on the pdbs object, using the “core atom indices” contained in core.
    pc.xray
    is a list object containing PCA results obtained by running the function pca.xyz on the “core fitted coordinates” contained in the xyz object.
    sse
    secondary structure annotation of a representative kineisn structure, 1bg2, as obtained from the function dssp

Source

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).

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. Grant, B.J. et al. (2007) J. Mol. Biol. 368, 1231–1248.


[Package bio3d version 1.0-5 Index]