procoil-package {procoil} | R Documentation

## Prediction of Oligomerization of Coiled Coil Proteins

### Description

The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.

### Details

The package defines two S4 classes, `CCModel` and `CCProfile`. The former's purpose is to represent a coiled coil prediction model. The default model `PrOCoilModel` is pre-loaded when the package is loaded. An alternative model `PrOCoilModelBA` is also available. Other models can be loaded with the function `readCCModel`. The `predict` function is used to predict the oligomerization of one or more coiled coil sequences (which consist of a amino acid sequences and heptad registers aligned to them). The result is stored in a `CCProfile` object. The resulting prediction profile can be visualized with `plot`.

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

http://www.bioinf.jku.at/software/procoil/

Mahrenholz, C.C., Abfalter, I.G., Bodenhofer, U., Volkmer, R., and Hochreiter, S. (2011) Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach. Mol. Cell. Proteomics 10(5):M110.004994. DOI: 10.1074/mcp.M110.004994

### Examples

    ## display summary of default model
    PrOCoilModel

    ## predict oligomerization of GCN4 wildtype
    GCN4wt <- predict(PrOCoilModel,
                      "MKQLEDKVEELLSKNYHLENEVARLKKLV",
                      "abcdefgabcdefgabcdefgabcdefga")

    ## display result
    GCN4wt

    ## plot profile
    plot(GCN4wt)

    ## predict oligomerization of unknown sequence (Marcoil example)
    MarcoilEx <- predict(PrOCoilModel,
        "MGECDQLLVFMITSRVLVLSTLIIMDSRQVYLENLRQFAENLRQNIENVHSFLENLRADLENLRQKFPGKWYSAMPGRHG",
        "-------------------------------abcdefgabcdefgabcdefgabcdefgabcdefg--------------")

    ## display result
    MarcoilEx

    ## plot profile
    plot(MarcoilEx)

[Package procoil version 2.20.0 Index]