ddG.profile

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

Contains utilities for the analysis of post-translational modifications (PTMs) in proteins,
with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download,
filter and analyze data from the sulfoxidation database 'MetOSite', and integrate data from other main PTMs
(other databases). Utilities to search and characterize S-aromatic motifs in proteins are also provided.
In addition, functions to analyze sequence environments around modifiable residues in proteins can be found.
For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable
residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
these differential sequence environments are also implemented. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).

Juan Aledo

Analyses of Protein Post-Translational Modifications

Juan Carlos Aledo

ddG.profile function

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

Arguments

Author

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

<dl>

<dt>prot</dt>
<dd>either the 4-letter identifier of a PDB structure, or the amino acid sequence (one letter amino acid code) of a protein.</dd>


<dt>ch</dt>
<dd>a letter identifying the chain of interest.</dd>


<dt>pos</dt>
<dd>the position, in the primary structure, of the residue to be mutated.</dd>


<dt>pH</dt>
<dd>a numeric value between 0 and 14.</dd>


<dt>Te</dt>
<dd>a numeric value indicating the temperature in degrees Celsius.</dd>

</dl>

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

Description

Usage

Value

Arguments

Author

Details

See Also

Examples