aaindex3: Statistical protein contact potentials matrices from AAindex...

In genomaths/GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations

Statistical protein contact potentials matrices from AAindex ver.9.2

Description

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.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex1, aaindex2, and get_mutscore.

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]

genomaths/GenomAutomorphism documentation built on Dec. 12, 2024, 2:12 p.m.