\name{procoil-package} \alias{procoil-package} \alias{procoil} \docType{package} \title{Prediction of Oligomerization of Coiled Coil Proteins} \description{ The \pkg{procoil} package allows to predict 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. The predict function not only computes the prediction itself, but also a profile which allows to determine the strengths to which the individual residues are indicative for either class. Profiles can also be visualized graphically using a plot function. } \details{ The package defines two S4 classes, \code{\linkS4class{CCModel}} and \code{\linkS4class{CCProfile}}. The former's purpose to represent a coiled coil prediction model. The default model \code{\link{PrOCoilModel}} is pre-loaded when the package is loaded. An alternative model \code{\link{PrOCoilModelBA}} can be loaded on demand. Other models can be loaded with the function \code{\link{readCCModel}}. The \code{\link[=predict,CCModel-method]{predict}} function is used to predict the oligomerization of a coiled coil sequence (which consists of an amino acid sequence and a heptad register aligned to it). The result is stored in a \code{\linkS4class{CCProfile}} object. The resulting prediction profile can be visualized with \code{\link[=plot,CCProfile,missing-method]{plot}}. } \author{Ulrich Bodenhofer \email{bodenhofer@bioinf.jku.at}} \references{\url{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. DOI: 10.1074/mcp.M110.004994} \keyword{ package } \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[[1]] ## plot profile plot(MarcoilEx[[1]]) }