LOGICOIL (version 0.99.0)

Model_Parameters: Model parameters for the LOGICOIL prediction algorithm.

Description

A list containing five elements, each of which are required to run the LOGICOIL prediction algorithm.

Usage

data(Model_Parameters)

Format

A list containing five elements, which are required to run the LOGICOIL model:

1. amino: a character vector containing allowed amino-acids.
2. register: a character vector containing allowed register assignments.
3. amino_interactions: a 87 x 2 matrix containing all amino-amino interactions considered in the LOGICOIL model.
4. register_interactions: a 87 x 2 matrix containing the matching register positions of the amino-amino interactions.
5. lag_matrix: a 7 x 7 matrix that gives the positional lag between register positions.

Source

DOI: 10.1093/bioinformatics/bts648

References

Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. "LOGICOIL-multi-state prediction of coiled-coil oligomeric state", 29(1), pp69-76, Bioinformatics, (2013). DOI: 10.1093/bioinformatics/bts648

Examples

data(Model_Parameters)
names(Model_Parameters)

# Optional to run
# summary(Model_Parameters$amino)
# summary(Model_Parameters$register)
# head(Model_Parameters$amino_interactions, 5)
# head(Model_Parameters$register_interactions, 5)
# Model_Parameters$lag_matrix