R: AAindex: Amino Acid Index Database

aa.index {bio3d} | R Documentation

## AAindex: Amino Acid Index Database

### Description

A collection of published indices, or scales, of numerous physicochemical and biological properties of the 20 standard aminoacids (Release 9.1, August 2006).

### Usage

    data(aa.index)

### Format

A list of 544 named indeces each with the following components:

1. H character vector: Accession number.

2. D character vector: Data description.

3. R character vector: LITDB entry number.

4. A character vector: Author(s).

5. T character vector: Title of the article.

6. J character vector: Journal reference.

7. 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.

8. I named numeric vector: Amino acid index data.

### Source

‘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.

### References

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.

### Examples

    ## 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

    ## 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)

[Package bio3d version 2.3-3 Index]