HEC_MI {DECIPHER} | R Documentation

## Mutual Information for Protein Secondary Structure Prediction

### Description

Arrays containing values of mutual information for single residues (`HEC_MI1`) and pairs of residues (`HEC_MI2`) located within 10 residues of the position being predicted (position "0"). The arrays have dimensions corresponding to the 20 (standard) amino acids, positions (-10 to 10), and states (helix ("H"), sheet ("E"), or coil ("C")).

### Usage

    data("HEC_MI1")
    data("HEC_MI2")

### Format

The format of HEC_MI1 is: num [1:20, 1:21, 1:3] 0.04264 -0.00117 0.02641 0.08264 -0.04876 ... - attr(*, "dimnames")=List of 3 ..$ : chr [1:20] "A" "R" "N" "D" ... ..$ : chr [1:21] "-10" "-9" "-8" "-7" ... ..$ : chr [1:3] "H" "E" "C"

The format of HEC_MI2 is: num [1:20, 1:20, 1:21, 1:21, 1:3] 2.56 -Inf -Inf -Inf -Inf ... - attr(*, "dimnames")=List of 5 ..$ : chr [1:20] "A" "R" "N" "D" ... ..$ : chr [1:20] "A" "R" "N" "D" ... ..$ : chr [1:21] "-10" "-9" "-8" "-7" ... ..$ : chr [1:21] "-10" "-9" "-8" "-7" ... ..$ : chr [1:3] "H" "E" "C"

### Details

The values in each matrix were derived based on a set of 15,201 proteins in the ASTRAL Compendium (Chandonia, 2004). The 8-states assigned by the Dictionary of Protein Secondary Structure (DSSP) were reduced to 3-states via H = G, H, or I; E = E; and C = B, S, C, or T.

### References

Chandonia, J. M. (2004). The ASTRAL Compendium in 2004. Nucleic Acids Research, 32(90001), 189D-192. doi:10.1093/nar/gkh034.

### Examples

    data(HEC_MI1)
    # the contribution of an arginine ("R")
    # located 3 residues left of center
    # to a helical ("H") state at the center
    HEC_MI1["R", "-3", "H"]

    data(HEC_MI2)
    # the contribution of arginine and lysine ("K")
    # located at positions -1 and +1, respectively
    # to a coil ("C") state at the center position
    HEC_MI2["R", "K", "-1", "1", "C"]

    matplot(-10:10, t(HEC_MI1[,, "H"]),
           type="l", col=1:8, lty=rep(1:3, each=8),
           xlab="Amino Acid Position Relative to Center",
           ylab="Log-Odds of Helix at Center Position")
    legend("bottomleft",
           lwd=1, col=1:8, lty=rep(1:3, each=8),
           legend=dimnames(HEC_MI1)[[1]], ncol=2)

[Package DECIPHER version 2.16.1 Index]