LOGICOIL: LOGICOIL: multi-state prediction of coiled-coil oligomeric state.

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This package contains the functions necessary to run the LOGICOIL algorithm. LOGICOIL can be used to differentiate between antiparallel dimers, parallel dimers, trimers and higher-order coiled-coil sequence. By covering >90 percent of the known coiled-coil structures, LOGICOIL is a net improvement compared with other existing methods, which achieve a predictive coverage of around 31 percent of this population. As such, LOGICOIL is particularly useful for researchers looking to characterize novel coiled-coil sequences or studying coiled-coil containing protein assemblies. It may also be used to assist in the structural characterization of synthetic coiled-coil sequences.

Author
Thomas L. Vincent <tlfvincent@gmail.com>, Peter J. Green and Derek N. Woolfson <D.N.Woolfson@bristol.ac.uk>
Date of publication
2014-04-14 00:04:00
Maintainer
Thomas L. Vincent <tlfvincent@gmail.com>
License
GPL (>= 2)
Version
0.99.0
URLs

View on CRAN

Man pages

EstimateProbability
Estimate oligomeric state score at each position of the input...
LOGICOIL
Predict oligomerization state of coiled-coil sequences.
LOGICOILfit
Fit of the multinomial log-linear model obtained from the...
LOGICOIL-package
Predict oligomerization state of coiled-coil sequences.
Model_Parameters
Model parameters for the LOGICOIL prediction algorithm.
plot_LOGICOIL
Plot the LOGICOIL scores
pssm
Profile scoring matrix derived from the LOGICOIL training...

Files in this package

LOGICOIL
LOGICOIL/NAMESPACE
LOGICOIL/data
LOGICOIL/data/LOGICOILfit.rda
LOGICOIL/data/pssm.rda
LOGICOIL/data/Model_Parameters.rda
LOGICOIL/R
LOGICOIL/R/LOGICOIL.R
LOGICOIL/R/EstimateProbability.R
LOGICOIL/R/plot_LOGICOIL.R
LOGICOIL/MD5
LOGICOIL/DESCRIPTION
LOGICOIL/man
LOGICOIL/man/LOGICOIL.Rd
LOGICOIL/man/plot_LOGICOIL.Rd
LOGICOIL/man/EstimateProbability.Rd
LOGICOIL/man/LOGICOILfit.Rd
LOGICOIL/man/LOGICOIL-package.Rd
LOGICOIL/man/Model_Parameters.Rd
LOGICOIL/man/pssm.Rd