example.data {bio3d} | R Documentation

## Bio3d Example Data

### Description

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.

### Usage

    data(kinesin)
    data(transducin)
    data(hivp)

### Format

Three objects from analysis of the `kinesin` and `transducin` sequence and structure data:

1. 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`.

2. core is a list of class `"core"` obtained by running the function `core.find` on the `pdbs` object as described above.

3. 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")’.

### Source

A related but more extensive dataset formed the basis of the work described in (Grant, 2007) and (Yao & Grant, 2013) for `kinesin` and `transducin` examples, respectively.

### References

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.

[Package bio3d version 2.3-4 Index]