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.
The package defines two S4 classes,
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
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
The resulting prediction profile can be visualized with
Ulrich Bodenhofer [email protected]
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
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## 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)
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