procoil (version 2.0.2)

procoil-package: 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.

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)