ddG.profile: Contribution of a given position to changes in stability

In ptm: Analyses of Protein Post-Translational Modifications

Contribution of a given position to changes in stability

Description

Represents the sensitivity of a given position to changes in stability of a protein (DDG).

Usage

ddG.profile(prot, ch, pos, pH = 7, Te = 25)

Arguments

prot	either the 4-letter identifier of a PDB structure, or the amino acid sequence (one letter amino acid code) of a protein.
ch	a letter identifying the chain of interest.
pos	the position, in the primary structure, of the residue to be mutated.
pH	a numeric value between 0 and 14.
Te	a numeric value indicating the temperature in degrees Celsius.

Details

It must be remembered that DDG > 0 implies destabilizing change and DDG > 0 implies a stabilizing change.

Value

The function returns a dataframe with the DDG values (kcal/mol) for each alternative amino acid, and a barplot grouping the amino acids according to their physicochemical nature.

Author(s)

Juan Carlos Aledo

See Also

foldx.mut(), imutant()

Examples

## Not run: ddG.profile(prot = '1pga', ch = 'A', pos = 27)

ptm documentation built on Aug. 7, 2022, 5:05 p.m.