protr (version 1.7-4)

extractCTDCClass: CTD Descriptors - Composition (with customized amino acid classification support)

Description

This function calculates the Composition descriptor of the CTD descriptors, with customized amino acid classification support.

Usage

extractCTDCClass(x, aagroup1, aagroup2, aagroup3)

Value

A length k * 3 named vector, k is the number of amino acid properties used.

Arguments

x

A character vector, as the input protein sequence.

aagroup1

A named list which contains the first group of customized amino acid classification. See example below.

aagroup2

A named list which contains the second group of customized amino acid classification. See example below.

aagroup3

A named list which contains the third group of customized amino acid classification. See example below.

Author

Nan Xiao <https://nanx.me>

References

Inna Dubchak, Ilya Muchink, Stephen R. Holbrook and Sung-Hou Kim. Prediction of protein folding class using global description of amino acid sequence. Proceedings of the National Academy of Sciences. USA, 1995, 92, 8700-8704.

Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou Kim. Recognition of a Protein Fold in the Context of the SCOP classification. Proteins: Structure, Function and Genetics, 1999, 35, 401-407.

See Also

See extractCTDTClass and extractCTDDClass for Transition and Distribution of the CTD descriptors with customized amino acid classification support.

Examples

x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]

# using five customized amino acid property classification
group1 <- list(
  "hydrophobicity" = c("R", "K", "E", "D", "Q", "N"),
  "normwaalsvolume" = c("G", "A", "S", "T", "P", "D", "C"),
  "polarizability" = c("G", "A", "S", "D", "T"),
  "secondarystruct" = c("E", "A", "L", "M", "Q", "K", "R", "H"),
  "solventaccess" = c("A", "L", "F", "C", "G", "I", "V", "W")
)

group2 <- list(
  "hydrophobicity" = c("G", "A", "S", "T", "P", "H", "Y"),
  "normwaalsvolume" = c("N", "V", "E", "Q", "I", "L"),
  "polarizability" = c("C", "P", "N", "V", "E", "Q", "I", "L"),
  "secondarystruct" = c("V", "I", "Y", "C", "W", "F", "T"),
  "solventaccess" = c("R", "K", "Q", "E", "N", "D")
)

group3 <- list(
  "hydrophobicity" = c("C", "L", "V", "I", "M", "F", "W"),
  "normwaalsvolume" = c("M", "H", "K", "F", "R", "Y", "W"),
  "polarizability" = c("K", "M", "H", "F", "R", "Y", "W"),
  "secondarystruct" = c("G", "N", "P", "S", "D"),
  "solventaccess" = c("M", "S", "P", "T", "H", "Y")
)

extractCTDCClass(x, aagroup1 = group1, aagroup2 = group2, aagroup3 = group3)