Mutual Information for Protein Secondary Structure Prediction

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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

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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

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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)

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