data(aaindex)
Kawashima, S. and Kanehisa, M. (2000) AAindex: amino acid index database. Nucleic Acids Res., 28:374. Tomii, K. and Kanehisa, M. (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng., 9:27-36. Nakai, K., Kidera, A., and Kanehisa, M. (1988) Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2:93-100.
#
# Load data:
#
data(aaindex)
#
# Supose that we need the Kyte & Doolittle Hydrophaty index. We first look
# at the entries with Kyte as author:
#
which(sapply(aaindex, function(x) length(grep("Kyte", x$A)) != 0))
#
# This should return that entry number 151 named KYTJ820101 is the only
# one that fit our request. We can access to it by position or by name,
# for instance:
#
aaindex[[151]]$I
aaindex[["KYTJ820101"]]$I
aaindex$KYTJ820101$I
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