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Statistical protein contact potentials matrices from AAindex ver.9.2

Source: R/data_aaindex3.R
aaindex3.Rd

A statistical potential (also knowledge-based potential, empirical potential, or residue contact potential) is an energy function derived from an analysis of known structures in the Protein Data Bank.

Usage

data("aaindex3", package = "GenomAutomorphism")

Format

A list carrying the the description 47 Amino Acid Matrices in AAindex ver.9.2 and the text file of matrices imported from https://www.genome.jp/aaindex/.

Details

A list of 47 amino acid matrices from Amino Acid Index Database https://www.genome.jp/aaindex/ are provided here. AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.

The contact potential matrix of amino acids is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches.

See also

aaindex1, aaindex2, and get_mutscore.

Author

Robersy Sanchez https://genomaths.com

Examples

## Load the mutation matrices from database from the packages
data("aaindex3", package = "GenomAutomorphism")

## Get the available mutation matrices
mat <- aa_mutmat(aaindex = "aaindex3", acc_list = TRUE)
mat[1:10]
#>  [1] "List of 47 Amino Acid Matrices in AAindex ver.9.2"                                                                 
#>  [2] ""                                                                                                                  
#>  [3] "The columns correspond to the AAindex accession number and the description of"                                     
#>  [4] "each contact potential matrix."                                                                                    
#>  [5] ""                                                                                                                  
#>  [6] "TANS760101 Statistical contact potential derived from 25 x-ray protein structures"                                 
#>  [7] "TANS760102 Number of contacts between side chains derived from 25 x-ray protein structures"                        
#>  [8] "ROBB790102 Interaction energies derived from side chain contacts in the interiors of known protein structures"     
#>  [9] "BRYS930101 Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)"
#> [10] "THOP960101 Mixed quasichemical and optimization-based protein contact potential"