SCORER2: SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

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This package contains the functions necessary to run the SCORER 2.0 algorithm. SCORER 2.0 can be used to differentiate between parallel dimeric and trimeric coiled-coil sequence, which are the two most more frequent coiled-coil structures observed naturally. As such, SCORER 2.0 is particularly useful for researchers looking to characterize novel coiled-coil sequences. It may also be used to assist in the structural characterization of synthetic coiled-coil sequences. Also included in this package are functions that allows the user to retrain the SCORER 2.0 algorithm using user-defined training data.

Author
Craig T. Armstrong, Thomas L. Vincent <tlfvincent@gmail.com>, Peter J. Green and Derek N. Woolfson <D.N.Woolfson@bristol.ac.uk>
Date of publication
2014-01-17 06:10:40
Maintainer
Thomas L. Vincent <tlfvincent@gmail.com>
License
GPL (>= 2)
Version
0.99.0
URLs

View on CRAN

Man pages

CreatePssm
Compute profile scoring matrices for training data
EstimateProbability
Estimate oligomeric state score of coiled-coil sequences
pssm
Profile scoring matrix derived from the original SCORER 2.0...
RetrainScorer2
Retrain the SCORER 2.0 algorithm with user-defined training...
scorer2
Predict oligomerization state of coiled-coil sequences
scorer-package
Predict oligomerization state of coiled-coil sequences
training
Training dataset used to contruct the profile scoring matrix...

Files in this package

SCORER2
SCORER2/NAMESPACE
SCORER2/data
SCORER2/data/pssm.RData
SCORER2/data/training.RData
SCORER2/R
SCORER2/R/scorer2.R
SCORER2/R/RetrainScorer2.R
SCORER2/R/EstimateProbability.R
SCORER2/R/CreatePssm.R
SCORER2/MD5
SCORER2/DESCRIPTION
SCORER2/man
SCORER2/man/CreatePssm.Rd
SCORER2/man/scorer-package.Rd
SCORER2/man/EstimateProbability.Rd
SCORER2/man/training.Rd
SCORER2/man/scorer2.Rd
SCORER2/man/RetrainScorer2.Rd
SCORER2/man/pssm.Rd