aa.index.RdA collection of published indices, or scales, of numerous physicochemical and biological properties of the 20 standard aminoacids (Release 9.1, August 2006).
data(aa.index)
A list of 544 named indeces each with the following components:
H character vector: Accession number.
D character vector: Data description.
R character vector: LITDB entry number.
A character vector: Author(s).
T character vector: Title of the article.
J character vector: Journal reference.
C named numeric vector: Correlation coefficients of similar indeces (with coefficients of 0.8/-0.8 or more/less). The correlation coefficient is calculated with zeros filled for missing values.
I named numeric vector: Amino acid index data.
‘AAIndex’ was obtained from:
http://www.genome.jp/aaindex/
For a description of the ‘AAindex’ database see:
http://www.genome.jp/aaindex/aaindex_help.html.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
‘AAIndex’ is the work of Kanehisa and co-workers:
Kawashima and Kanehisa (2000) Nucleic Acids Res. 28, 374;
Tomii and Kanehisa (1996) Protein Eng. 9, 27--36;
Nakai, Kidera and Kanehisa (1988) Protein Eng. 2, 93--100.
## Load AAindex data data(aa.index) ## Find all indeces described as "volume" ind <- which(sapply(aa.index, function(x) length(grep("volume", x$D, ignore.case=TRUE)) != 0)) ## find all indeces with author "Kyte" ind <- which(sapply(aa.index, function(x) length(grep("Kyte", x$A)) != 0)) ## examine the index aa.index[[ind]]$I#> A R N D C Q E G H I L K M F P S #> 1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5 3.8 -3.9 1.9 2.8 -1.6 -0.8 #> T W Y V #> -0.7 -0.9 -1.3 4.2## find indeces which correlate with it all.ind <- names(which(Mod(aa.index[[ind]]$C) >= 0.88)) ## examine them all sapply(all.ind, function (x) aa.index[[x]]$I)#> JURD980101 CHOC760103 OLSK800101 JANJ780102 NADH010102 NADH010101 DESM900102 #> A 1.10 0.38 1.38 51 51 58 1.26 #> R -5.10 0.01 0.00 5 -144 -184 0.38 #> N -3.50 0.12 0.37 22 -84 -93 0.59 #> D -3.60 0.15 0.52 19 -78 -97 0.27 #> C 2.50 0.45 1.43 74 137 116 1.60 #> Q -3.68 0.07 0.22 16 -128 -139 0.39 #> E -3.20 0.18 0.71 16 -115 -131 0.23 #> G -0.64 0.36 1.34 52 -13 -11 1.08 #> H -3.20 0.17 0.66 34 -55 -73 1.00 #> I 4.50 0.60 2.32 66 106 107 1.44 #> L 3.80 0.45 1.47 60 103 95 1.36 #> K -4.11 0.03 0.15 3 -205 -24 0.33 #> M 1.90 0.40 1.78 52 73 78 1.52 #> F 2.80 0.50 1.72 58 108 92 1.46 #> P -1.90 0.18 0.85 25 -79 -79 0.54 #> S -0.50 0.22 0.86 35 -26 -34 0.98 #> T -0.70 0.23 0.89 30 -3 -7 1.01 #> W -0.46 0.27 0.82 49 69 59 1.06 #> Y -1.30 0.15 0.47 24 11 -11 0.89 #> V 4.20 0.54 1.99 64 108 100 1.33 #> EISD860103 CHOC760104 NADH010103 WOLR810101 RADA880101 MANP780101 KUHL950101 #> A 0.00 0.20 41 1.94 1.81 12.97 0.78 #> R -0.96 0.00 -109 -19.92 -14.92 11.72 1.58 #> N -0.86 0.03 -74 -9.68 -6.64 11.42 1.20 #> D -0.98 0.04 -47 -10.95 -8.72 10.85 1.35 #> C 0.76 0.22 169 -1.24 1.28 14.63 0.55 #> Q -1.00 0.01 -104 -9.38 -5.54 11.76 1.19 #> E -0.89 0.03 -90 -10.20 -6.81 11.89 1.45 #> G 0.00 0.18 -18 2.39 0.94 12.43 0.68 #> H -0.75 0.02 -35 -10.27 -4.66 12.16 0.99 #> I 0.99 0.19 104 2.15 4.92 15.67 0.47 #> L 0.89 0.16 103 2.28 4.92 14.90 0.56 #> K -0.99 0.00 -148 -9.52 -5.55 11.36 1.10 #> M 0.94 0.11 77 -1.48 2.35 14.39 0.66 #> F 0.92 0.14 128 -0.76 2.98 14.00 0.47 #> P 0.22 0.04 -81 -3.68 0.00 11.37 0.69 #> S -0.67 0.08 -31 -5.06 -3.40 11.23 1.00 #> T 0.09 0.08 10 -4.88 -2.57 11.69 1.05 #> W 0.67 0.04 102 -5.88 2.33 13.93 0.70 #> Y -0.93 0.03 36 -6.11 -0.14 13.42 1.00 #> V 0.84 0.18 116 1.99 4.04 15.71 0.51 #> GUYH850105 OOBM770101 #> A -0.27 -1.895 #> R 2.00 -1.475 #> N 0.61 -1.560 #> D 0.50 -1.518 #> C -0.23 -2.035 #> Q 1.00 -1.521 #> E 0.33 -1.535 #> G -0.22 -1.898 #> H 0.37 -1.755 #> I -0.80 -1.951 #> L -0.44 -1.966 #> K 1.17 -1.374 #> M -0.31 -1.963 #> F -0.55 -1.864 #> P 0.36 -1.699 #> S 0.17 -1.753 #> T 0.18 -1.767 #> W 0.05 -1.869 #> Y 0.48 -1.686 #> V -0.65 -1.981