Computes changes in the stability of a protein after a residue mutation using a machine-learning approach.
imutant(protein, ch = "_", pos, newres = "", pH = 7, Te = 25, timeout = 60)either the 4-letter identifier of a PDB structure, or the amino acid sequence (one letter amino acid code) of a protein.
a letter identifying the chain of interest.
the position, in the primary structure, of the residue to be mutated.
the one letter code of the residue to be incorporated. When a value is not entered for this parameter, then the function will compute DDG for the mutation to any possible amino acid.
a numeric value between 0 and 14.
a numeric value indicating the temperature in degrees Celsius.
maximum time to wait, in seconds, for a response from the I-Mutant server.
The function computes and returns a dataframe containing the following variables:
Position: Position in the primary structure of the mutated residue.
WT: Amino acid found at that position in the wild-type protein.
NW: New amino acid found in the mutated protein.
DDG: Change in Gibbs free energy (kcal/mol), defined as DDG = DGmt - DGwt, where DG is the change in Gibbs free energy for the folding of the protein from its unfolded state. Thus, a positive value means a stabilizing effect, and vice versa.
pH: -log[H+]
T: Temperature in Celsius degrees.
RSA: Relative Solvent Accessible Area (Only if a PDB file has been provided).
This function implements the I-Mutant v2.0 tool, which is a fast method based on a support vector machine approach to predict protein stability changes upon single point mutations.
Capriotti et al (2005) Nucl. Ac. Res. 33:W306-W310.
foldx.mut(), ddG.profile()
# NOT RUN {
imutant(protein = '1u8f', ch = 'O', pos = 46, newres = 'K')
# }
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