\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]])
}