Model_Parameters: Model parameters for the LOGICOIL prediction algorithm.

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

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

LOGICOIL documentation built on May 2, 2019, 9:09 a.m.