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SCORER2 (version 0.99.0)

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

Description

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.

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Version

Install

install.packages('SCORER2')

Monthly Downloads

8

Version

0.99.0

License

GPL (>= 2)

Maintainer

Thomas L Vincent

Last Published

January 17th, 2014

Functions in SCORER2 (0.99.0)

CreatePssm

Compute profile scoring matrices for training data
scorer2-package

Predict oligomerization state of coiled-coil sequences
training

Training dataset used to contruct the profile scoring matrix in the SCORER 2.0 algorithm.
EstimateProbability

Estimate oligomeric state score of coiled-coil sequences
pssm

Profile scoring matrix derived from the original SCORER 2.0 training set.
RetrainScorer2

Retrain the SCORER 2.0 algorithm with user-defined training data
scorer2

Predict oligomerization state of coiled-coil sequences